bayes1_manuscript.bib

@misc{smirnoff,
  title = {The SMIRks Native Open Force Field (SMIRNOFF) GitHub Repository},
  howpublished = {\url{https://github.com/open-forcefield-group/smirnoff99Frosst}},
  note = {Accessed: 2017-03-09}
}

@article{bayes1,
	title = {A {Bayesian} framework for adaptive selection, calibration, and validation of coarse-grained models of atomistic systems},
	volume = {295},
	issn = {0021-9991},
	url = {http://www.sciencedirect.com/science/article/pii/S0021999115002430},
	doi = {10.1016/j.jcp.2015.03.071},
	abstract = {A general adaptive modeling algorithm for selection and validation of coarse-grained models of atomistic systems is presented. A Bayesian framework is developed to address uncertainties in parameters, data, and model selection. Algorithms for computing output sensitivities to parameter variances, model evidence and posterior model plausibilities for given data, and for computing what are referred to as Occam Categories in reference to a rough measure of model simplicity, make up components of the overall approach. Computational results are provided for representative applications.},
	urldate = {2017-03-09},
	journal = {Journal of Computational Physics},
	author = {Farrell, Kathryn and Oden, J. Tinsley and Faghihi, Danial},
	month = aug,
	year = {2015},
	keywords = {Bayesian inference, Coarse graining models, Model plausibility, Model validation, Output sensitivities},
	pages = {189--208},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\Bryce Manubay\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\fjrkfkzw.default\\zotero\\storage\\ZXH8AIIX\\Farrell et al. - 2015 - A Bayesian framework for adaptive selection, calib.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Bryce Manubay\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\fjrkfkzw.default\\zotero\\storage\\8XHVTK9H\\S0021999115002430.html:text/html}
}

@article{bayes2,
	title = {A {Bayesian} {Modelling} {Approach} with {Balancing} {Informative} {Prior} for {Analysing} {Imbalanced} {Data}},
	volume = {11},
	issn = {1932-6203},
	url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0152700},
	doi = {10.1371/journal.pone.0152700},
	abstract = {When a dataset is imbalanced, the prediction of the scarcely-sampled subpopulation can be over-influenced by the population contributing to the majority of the data. The aim of this study was to develop a Bayesian modelling approach with balancing informative prior so that the influence of imbalance to the overall prediction could be minimised. The new approach was developed in order to weigh the data in favour of the smaller subset(s). The method was assessed in terms of bias and precision in predicting model parameter estimates of simulated datasets. Moreover, the method was evaluated in predicting optimal dose levels of tobramycin for various age groups in a motivating example. The bias estimates using the balancing informative prior approach were smaller than those generated using the conventional approach which was without the consideration for the imbalance in the datasets. The precision estimates were also superior. The method was further evaluated in a motivating example of optimal dosage prediction of tobramycin. The resulting predictions also agreed well with what had been reported in the literature. The proposed Bayesian balancing informative prior approach has shown a real potential to adequately weigh the data in favour of smaller subset(s) of data to generate robust prediction models.},
	number = {4},
	urldate = {2016-10-08},
	journal = {PLOS ONE},
	author = {Klein, Kerenaftali and Hennig, Stefanie and Paul, Sanjoy Ketan},
	month = apr,
	year = {2016},
	keywords = {Age distribution, Age groups, Cystic fibrosis, Dose prediction methods, Forecasting, Infants, Pediatrics, Simulation and modeling},
	pages = {e0152700},
	file = {Full Text PDF:C\:\\Users\\Bryce Manubay\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\fjrkfkzw.default\\zotero\\storage\\3FWVV828\\Klein et al. - 2016 - A Bayesian Modelling Approach with Balancing Infor.pdf:application/pdf;Snapshot:C\:\\Users\\Bryce Manubay\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\fjrkfkzw.default\\zotero\\storage\\PG6JWXN5\\article.html:text/html}
}

@article{bayes3,
	title = {A hierarchical {Bayesian} framework for force field selection in molecular dynamics simulations},
	volume = {374},
	copyright = {© 2015 The Author(s). http://royalsocietypublishing.org/licence},
	issn = {1364-503X, 1471-2962},
	url = {http://rsta.royalsocietypublishing.org/content/374/2060/20150032},
	doi = {10.1098/rsta.2015.0032},
	abstract = {We present a hierarchical Bayesian framework for the selection of force fields in molecular dynamics (MD) simulations. The framework associates the variability of the optimal parameters of the MD potentials under different environmental conditions with the corresponding variability in experimental data. The high computational cost associated with the hierarchical Bayesian framework is reduced by orders of magnitude through a parallelized Transitional Markov Chain Monte Carlo method combined with the Laplace Asymptotic Approximation. The suitability of the hierarchical approach is demonstrated by performing MD simulations with prescribed parameters to obtain data for transport coefficients under different conditions, which are then used to infer and evaluate the parameters of the MD model. We demonstrate the selection of MD models based on experimental data and verify that the hierarchical model can accurately quantify the uncertainty across experiments; improve the posterior probability density function estimation of the parameters, thus, improve predictions on future experiments; identify the most plausible force field to describe the underlying structure of a given dataset. The framework and associated software are applicable to a wide range of nanoscale simulations associated with experimental data with a hierarchical structure.},
	language = {en},
	number = {2060},
	urldate = {2017-02-23},
	journal = {Phil. Trans. R. Soc. A},
	author = {Wu, S. and Angelikopoulos, P. and Papadimitriou, C. and Moser, R. and Koumoutsakos, P.},
	month = feb,
	year = {2016},
	pmid = {26712642},
	pages = {20150032},
	file = {Full Text PDF:C\:\\Users\\Bryce Manubay\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\fjrkfkzw.default\\zotero\\storage\\HB8QRTCV\\Wu et al. - 2016 - A hierarchical Bayesian framework for force field .pdf:application/pdf;Snapshot:C\:\\Users\\Bryce Manubay\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\fjrkfkzw.default\\zotero\\storage\\E6P5HR44\\20150032.html:text/html}
}

@article{bayes4,
	title = {Bayesian uncertainty quantification and propagation in molecular dynamics simulations: {A} high performance computing framework},
	volume = {137},
	issn = {0021-9606},
	shorttitle = {Bayesian uncertainty quantification and propagation in molecular dynamics simulations},
	url = {http://aip.scitation.org/doi/10.1063/1.4757266},
	doi = {10.1063/1.4757266},
	abstract = {We present a Bayesian probabilistic framework for quantifying and propagating the uncertainties in the parameters of force fields employed in molecular dynamics (MD) simulations. We propose a highly parallel implementation of the transitional Markov chain Monte Carlo for populating the posterior probability distribution of the MD force-field parameters. Efficient scheduling algorithms are proposed to handle the MD model runs and to distribute the computations in clusters with heterogeneous architectures. Furthermore, adaptive surrogate models are proposed in order to reduce the computational cost associated with the large number of MD model runs. The effectiveness and computational efficiency of the proposed Bayesian framework is demonstrated in MD simulations of liquid and gaseous argon.},
	number = {14},
	urldate = {2017-03-09},
	journal = {The Journal of Chemical Physics},
        author = {Angelikopoulos, Panagiotis and Papadimitriou, Costas and Koumoutsakos, Petros},
	month = oct,
	year = {2012},
	pages = {144103},
	file = {Full Text PDF:C\:\\Users\\Bryce Manubay\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\fjrkfkzw.default\\zotero\\storage\\9P33NI2Z\\2012 - Bayesian uncertainty quantification and propagatio.pdf:application/pdf;Snapshot:C\:\\Users\\Bryce Manubay\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\fjrkfkzw.default\\zotero\\storage\\XNMIPB5F\\1.html:text/html}
}

@article{bayes5,
	title = {Big {Learning} with {Bayesian} {Methods}},
	url = {http://arxiv.org/abs/1411.6370},
	abstract = {Explosive growth in data and availability of cheap computing resources have sparked increasing interest in Big learning, an emerging subfield that studies scalable machine learning algorithms, systems, and applications with Big Data. Bayesian methods represent one important class of statistic methods for machine learning, with substantial recent developments on adaptive, flexible and scalable Bayesian learning. This article provides a survey of the recent advances in Big learning with Bayesian methods, termed Big Bayesian Learning, including nonparametric Bayesian methods for adaptively inferring model complexity, regularized Bayesian inference for improving the flexibility via posterior regularization, and scalable algorithms and systems based on stochastic subsampling and distributed computing for dealing with large-scale applications.},
	urldate = {2017-03-09},
	journal = {arXiv:1411.6370 [cs, stat]},
	author = {Zhu, Jun and Chen, Jianfei and Hu, Wenbo and Zhang, Bo},
	month = nov,
	year = {2014},
	note = {arXiv: 1411.6370},
	keywords = {Computer Science - Learning, F.1.2, G.3, Statistics - Applications, Statistics - Computation, Statistics - Machine Learning, Statistics - Methodology},
	file = {arXiv\:1411.6370 PDF:C\:\\Users\\Bryce Manubay\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\fjrkfkzw.default\\zotero\\storage\\7XIFMCGA\\Zhu et al. - 2014 - Big Learning with Bayesian Methods.pdf:application/pdf;arXiv.org Snapshot:C\:\\Users\\Bryce Manubay\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\fjrkfkzw.default\\zotero\\storage\\CXXXWZD3\\1411.html:text/html}
}

@article{bayes6,
	title = {Calibration of forcefields for molecular simulation: {Sequential} design of computer experiments for building cost-efficient kriging metamodels},
	volume = {35},
	issn = {1096-987X},
	shorttitle = {Calibration of forcefields for molecular simulation},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/jcc.23475/abstract},
	doi = {10.1002/jcc.23475},
	abstract = {We present a global strategy for molecular simulation forcefield optimization, using recent advances in Efficient Global Optimization algorithms. During the course of the optimization process, probabilistic kriging metamodels are used, that predict molecular simulation results for a given set of forcefield parameter values. This enables a thorough investigation of parameter space, and a global search for the minimum of a score function by properly integrating relevant uncertainty sources. Additional information about the forcefield parameters are obtained that are inaccessible with standard optimization strategies. In particular, uncertainty on the optimal forcefield parameters can be estimated, and transferred to simulation predictions. This global optimization strategy is benchmarked on the TIP4P water model. © 2013 Wiley Periodicals, Inc.},
	language = {en},
	number = {2},
	urldate = {2017-02-23},
	journal = {J. Comput. Chem.},
	author = {Cailliez, Fabien and Bourasseau, Arnaud and Pernot, Pascal},
	month = jan,
	year = {2014},
	keywords = {efficient global optimization, forcefield calibration, kriging, Molecular simulation, uncertainty quantification},
	pages = {130--149},
	file = {Full Text PDF:C\:\\Users\\Bryce Manubay\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\fjrkfkzw.default\\zotero\\storage\\U7QTS6QM\\Cailliez et al. - 2014 - Calibration of forcefields for molecular simulatio.pdf:application/pdf;Snapshot:C\:\\Users\\Bryce Manubay\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\fjrkfkzw.default\\zotero\\storage\\CR47Q22T\\abstract.html:text/html}
}

@book{bayes7,
	title = {Monte {Carlo} {Strategies} in {Scientific} {Computing}},
        author = {Jun S. Liu},
        publisher = {Springer},
        year = {2001},
	url = {http://www.springer.com/us/book/9780387763699},
	abstract = {This paperback edition is a reprint of the 2001 Springer edition.

This book provides a self-contained and up-to-date treatment of the Monte Carlo method...},
	urldate = {2017-03-09},
	file = {Snapshot:C\:\\Users\\Bryce Manubay\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\fjrkfkzw.default\\zotero\\storage\\8S7Q6VR6\\9780387763699.html:text/html}
}
@book{bayes8,
	title = {Bayesian Inference in Statistical Analysis},
        author = {Box, George E.P. and Tiao, George C.},
	publisher = {John Wiley & Sons, Inc.},
	isbn = {9781118033197},
	url = {http://dx.doi.org/10.1002/9781118033197.fmatter},
	doi = {10.1002/9781118033197.fmatter},
	year = {1992},
}

@article{monticelli,
	title = {Force fields for classical molecular dynamics},
	volume = {924},
	issn = {1940-6029},
	doi = {10.1007/978-1-62703-017-5_8},
	abstract = {In this chapter we review the basic features and the principles underlying molecular mechanics force fields commonly used in molecular modeling of biological macromolecules. We start by summarizing the historical background and then describe classical pairwise additive potential energy functions. We introduce the problem of the calculation of nonbonded interactions, of particular importance for charged macromolecules. Different parameterization philosophies are then presented, followed by a section on force field validation. We conclude with a brief overview on future perspectives for the development of classical force fields.},
	language = {eng},
	journal = {Methods Mol. Biol.},
	author = {Monticelli, Luca and Tieleman, D. Peter},
	year = {2013},
	pmid = {23034750},
	keywords = {Biopolymers, Mathematical Concepts, Molecular Dynamics Simulation, Reproducibility of Results},
	pages = {197--213}
}

@article{aipar,
	title = {{AIPAR}: ab initio parametrization of intermolecular potentials for computer simulations},
	volume = {11},
	issn = {1610-2940, 0948-5023},
	shorttitle = {{AIPAR}},
	url = {https://link.springer.com/article/10.1007/s00894-004-0222-9},
	doi = {10.1007/s00894-004-0222-9},
	abstract = {An unambiguous, fully ab initio and automated technique denoted AIPAR (“ab initio parametrization”) implemented in the SJBR program has been proposed to yield intermolecular interaction potentials between polar molecules and water. The AIPAR procedure has been applied to several organic molecules covering a wide range of structure and functional groups, namely methanol, acetone (propanone), methanethiol (methyl mercaptan), imidazole (1,3-diazole), oxazole and furan. The AIPAR-derived sets of parameters compare well with the empirical OPLS ones, mainly when the all-atoms model is employed in the OPLS procedure. Monte Carlo simulations were performed for an aqueous solution of methanol and for an equimolar binary mixture methanol–water using the AIPAR and OPLS parameters. The thermodynamic and geometric results obtained with the parameters obtained with the AIPAR procedure compare favorably with the OPLS simulations, even for the binary mixture, demonstrating the precision, robustness and transferability of the parameters obtained with the AIPAR procedure.Figure Superimposed configurations of water (without the hydrogen atoms) around the methanol molecule obtained with the AGOA procedure.},
	language = {en},
	number = {1},
	urldate = {2017-03-09},
	journal = {J Mol Model},
	author = {Hernandes, Marcelo Z. and Longo, Ricardo L.},
	month = feb,
	year = {2005},
	pages = {61--68},
	file = {Full Text PDF:C\:\\Users\\Bryce Manubay\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\fjrkfkzw.default\\zotero\\storage\\3ZBUPVBH\\Hernandes and Longo - 2005 - AIPAR ab initio parametrization of intermolecular.pdf:application/pdf;Snapshot:C\:\\Users\\Bryce Manubay\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\fjrkfkzw.default\\zotero\\storage\\P23P4JSK\\s00894-004-0222-9.html:text/html}
}

@article{combined,
	title = {Combined ab initio/empirical approach for optimization of {Lennard}-{Jones} parameters for polar-neutral compounds},
	volume = {23},
	issn = {0192-8651},
	doi = {10.1002/jcc.1166},
	abstract = {The study of small functionalized organic molecules in aqueous solution is a useful step toward gaining a basic understanding of the behavior of biomolecular systems in their native aqueous environment. Interest in studying amines and fluorine-substituted compounds has risen from their intrinsic physicochemical properties and their prevalence in biological and pharmaceutical compounds. In the present study, a previously developed approach which optimizes Lennard-Jones (LJ) parameters via the use of rare gas atoms combined with the reproduction of experimental condensed phase properties was extended to polar-neutral compounds. Compounds studied included four amines (ammonia, methylamine, dimethylamine, and trimethylamine) and three fluoroethanes (1-fluoroethane, 1,1-difluoroethane, and 1,1,1-trifluoroethane). The resulting force field yielded heats of vaporization and molecular volumes in excellent agreement with the experiment, with average differences less than 1\%. The current amine CHARMM parameters successfully reproduced experimental aqueous solvation data where methylamine is more hydrophilic than ammonia, with hydrophobicity increasing with additional methylation on the nitrogen. For both the amines and fluoroethanes the parabolic relationship of the extent of methylation or fluorination, respectively, to the heats of vaporization were reproduced by the new parameters. The present results are also discussed with respect to the impact of parameterization approach to molecular details obtained from computer simulations and to the unique biological properties of fluorine in pharmaceutical compounds.},
	language = {eng},
	number = {2},
	journal = {J Comput Chem},
	author = {Chen, I. Jen and Yin, Daxu and MacKerell, Alexander D.},
	month = jan,
	year = {2002},
	pmid = {11924734},
	keywords = {Amines, Fluorides, Hydrophobic and Hydrophilic Interactions, Models, Molecular, Organic Chemicals, solubility, Static Electricity},
	pages = {199--213}
}

@article{tip3p,
	title = {Comparison of simple potential functions for simulating liquid water},
	volume = {79},
	issn = {0021-9606},
	url = {http://aip.scitation.org/doi/10.1063/1.445869},
	doi = {10.1063/1.445869},
	number = {2},
	urldate = {2017-03-09},
	journal = {The Journal of Chemical Physics},
        author = {Jorgensen, William L. and Chandrasekhar, Jayaraman and Madura, Jeffry D.},
	month = jul,
	year = {1983},
	pages = {926--935},
	file = {Full Text PDF:C\:\\Users\\Bryce Manubay\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\fjrkfkzw.default\\zotero\\storage\\NW9JP5JN\\1983 - Comparison of simple potential functions for simul.pdf:application/pdf;Snapshot:C\:\\Users\\Bryce Manubay\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\fjrkfkzw.default\\zotero\\storage\\Q79ZVCDA\\1.html:text/html}
}

@article{burger,
	title = {Efficient optimization of van der {Waals} parameters from bulk properties},
	volume = {34},
	issn = {1096-987X},
	doi = {10.1002/jcc.23376},
	abstract = {Due to the computational cost involved, when developing a force field for new compounds, one often avoids fitting van der Waals (vdW) terms, instead relying on a general force field based on the atom type. Here, we provide a novel approach to efficiently optimize vdW terms, based on both ab initio dimer energies and condensed phase properties. The approach avoids the computational challenges of searching the parameter space by using an extrapolation method to obtain a reliable difference quotient for the parameter derivatives based on the central difference. The derivatives are then used in an active-space optimization method which convergences quadratically. This method is applicable to polarizable and nonpolarizable force fields, although we focus on the parameterization of the AMBER force field. The scaling of the electrostatic potential (ESP) of the compounds is also studied. The algorithm is tested on 12 compounds, reducing the root mean squared error (RMSE) of the density from 0.061 g/cm(3) with GAFF parameters to 0.004 g/cm(3) , and the heat of vaporization from 1.13 to 0.05 kcal/mol. This is done with only four iterations of molecular dynamic runs. Using the optimized vdW parameters, the RMSE of the self-diffusion (Dself ) was reduced from 1.22 × 10(-9) to 0.78 × 10(-9) m(2) s(-1) and the RMSE of the hydration free energies (ΔGsolv ) was reduced from 0.30 to 0.26 kcal/mol. Scaling the ESP to improve dimer energies resulted in the Dself  RMSE improving to 0.77× 10(-9) m(2) s(-1) , but the ΔGsolv  worsened to 0.33 kcal/mol.},
	language = {eng},
	number = {27},
	journal = {J Comput Chem},
	author = {Burger, Steven K. and Cisneros, G. Andrés},
	month = oct,
	year = {2013},
	pmid = {23828265},
	keywords = {Algorithms, AMBER, bulk properties, Computer Simulation, Dimerization, Force field parameters, Models, Chemical, optimization, Organic Chemicals, Static Electricity, Thermodynamics, Van der Waals},
	pages = {2313--2319}
}

@article{rational,
	title = {Rational design of ion force fields based on thermodynamic solvation properties},
	volume = {130},
	issn = {0021-9606},
	url = {http://aip.scitation.org/doi/full/10.1063/1.3081142},
	doi = {10.1063/1.3081142},
	abstract = {solvation},
	number = {12},
	urldate = {2017-03-09},
	journal = {The Journal of Chemical Physics},
        author = {Horinek, Dominik and Mamatkulov, Shavkat I. and Netz, Roland R.},
	month = mar,
	year = {2009},
	pages = {124507},
	file = {Full Text PDF:C\:\\Users\\Bryce Manubay\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\fjrkfkzw.default\\zotero\\storage\\DAUVX86K\\2009 - Rational design of ion force fields based on therm.pdf:application/pdf;Snapshot:C\:\\Users\\Bryce Manubay\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\fjrkfkzw.default\\zotero\\storage\\6BI2JKXK\\1.html:text/html}
}

@article{law,
	title = "I-NoLLS: A program for interactive nonlinear least-squares fitting of the parameters of physical models",
	journal = "Computer Physics Communications",
	volume = "102",
	number = "1",
	pages = "252 - 268",
	year = "1997",
	note = "",
	issn = "0010-4655",
	doi = "http://dx.doi.org/10.1016/S0010-4655(97)00013-1",
	url = "http://www.sciencedirect.com/science/article/pii/S0010465597000131",
	author = "Mark M. Law and Jeremy M. Hutson",
	keywords = "Interactive",
	keywords = "Nonlinear least-squares",
	keywords = "Molecular potential energy surface",
	keywords = "Optimization",
	keywords = "Model fitting",
	abstract = "The I-NoLLS program is a package for carrying out interactive nonlinear least-squares fits to determine the parameters of physical or mathematical models from experimental or other data, under circumstances where automated least-squares procedures are excessively computationally expensive and the user needs interactive control to apply physical insight to the fitting process. The program was developed to facilitate the fitting of molecular potential energy surfaces (PES) to spectroscopic and scattering data, but is also applicable to a variety of other optimization problems. A range of different algorithms adapted to highly nonlinear least-squares problems may be selected. The interactive nature of the code permits rapid and flexible control over the progress of the fit. I-NoLLS is written in a modular way that allows the easy incorporation of new modules for calculating observable quantities from model parameters. The structure of the program allows straightforward parallelisation of the time-consuming property calculations. In pilot applications, I-NoLLS has been interfaced with programs for calculating bound states of Van der Waals complexes, cross sections for molecular scattering processes, and second virial coefficients of gas mixtures. Parallelisation of the property calculations has been achieved using PVM running on a cluster of workstations."
}

@article{ffcomp2,
	title = {Comparing {Molecular} {Dynamics} {Force} {Fields} in the {Essential} {Subspace}},
	volume = {10},
	issn = {1932-6203},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4374674/},
	doi = {10.1371/journal.pone.0121114},
	abstract = {The continued development and utility of molecular dynamics simulations requires improvements in both the physical models used (force fields) and in our ability to sample the Boltzmann distribution of these models. Recent developments in both areas have made available multi-microsecond simulations of two proteins, ubiquitin and Protein G, using a number of different force fields. Although these force fields mostly share a common mathematical form, they differ in their parameters and in the philosophy by which these were derived, and previous analyses showed varying levels of agreement with experimental NMR data. To complement the comparison to experiments, we have performed a structural analysis of and comparison between these simulations, thereby providing insight into the relationship between force-field parameterization, the resulting ensemble of conformations and the agreement with experiments. In particular, our results show that, at a coarse level, many of the motional properties are preserved across several, though not all, force fields. At a finer level of detail, however, there are distinct differences in both the structure and dynamics of the two proteins, which can, together with comparison with experimental data, help to select force fields for simulations of proteins. A noteworthy observation is that force fields that have been reparameterized and improved to provide a more accurate energetic description of the balance between helical and coil structures are difficult to distinguish from their “unbalanced” counterparts in these simulations. This observation implies that simulations of stable, folded proteins, even those reaching 10 microseconds in length, may provide relatively little information that can be used to modify torsion parameters to achieve an accurate balance between different secondary structural elements.},
	number = {3},
	urldate = {2016-10-06},
	journal = {PLoS One},
	author = {Mart{\'i}n-Garc{\'i}a, Fernando and Papaleo, Elena and Gomez-Puertas, Paulino and Boomsma, Wouter and Lindorff-Larsen, Kresten},
	month = mar,
	year = {2015},
	pmid = {25811178},
	pmcid = {PMC4374674},
	file = {PubMed Central Full Text PDF:files/17/Martín-García et al. - 2015 - Comparing Molecular Dynamics Force Fields in the E.pdf:application/pdf}
}

@article{drug_discov,
	title = {Role of {Molecular} {Dynamics} and {Related} {Methods} in {Drug} {Discovery}},
	volume = {59},
	issn = {0022-2623},
	url = {http://dx.doi.org/10.1021/acs.jmedchem.5b01684},
	doi = {10.1021/acs.jmedchem.5b01684},
	abstract = {Molecular dynamics (MD) and related methods are close to becoming routine computational tools for drug discovery. Their main advantage is in explicitly treating structural flexibility and entropic effects. This allows a more accurate estimate of the thermodynamics and kinetics associated with drug–target recognition and binding, as better algorithms and hardware architectures increase their use. Here, we review the theoretical background of MD and enhanced sampling methods, focusing on free-energy perturbation, metadynamics, steered MD, and other methods most consistently used to study drug–target binding. We discuss unbiased MD simulations that nowadays allow the observation of unsupervised ligand–target binding, assessing how these approaches help optimizing target affinity and drug residence time toward improved drug efficacy. Further issues discussed include allosteric modulation and the role of water molecules in ligand binding and optimization. We conclude by calling for more prospective studies to attest to these methods’ utility in discovering novel drug candidates.},
	number = {9},
	urldate = {2016-10-06},
	journal = {J. Med. Chem.},
	author = {De Vivo, Marco and Masetti, Matteo and Bottegoni, Giovanni and Cavalli, Andrea},
	month = may,
	year = {2016},
	pages = {4035--4061},
	file = {ACS Full Text PDF w/ Links:files/7/De Vivo et al. - 2016 - Role of Molecular Dynamics and Related Methods in .pdf:application/pdf;ACS Full Text Snapshot:files/8/acs.jmedchem.html:text/html}
}

@article{ffcomp1,
	title = {Scrutinizing {Molecular} {Mechanics} {Force} {Fields} on the {Submicrosecond} {Timescale} with {NMR} {Data}},
	volume = {99},
	issn = {0006-3495},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905107/},
	doi = {10.1016/j.bpj.2010.04.062},
	abstract = {Protein dynamics on the atomic level and on the microsecond timescale has recently become accessible from both computation and experiment. To validate molecular dynamics (MD) at the submicrosecond timescale against experiment we present microsecond MD simulations in 10 different force-field configurations for two globular proteins, ubiquitin and the gb3 domain of protein G, for which extensive NMR data is available. We find that the reproduction of the measured NMR data strongly depends on the chosen force field and electrostatics treatment. Generally, particle-mesh Ewald outperforms cut-off and reaction-field approaches. A comparison to measured J-couplings across hydrogen bonds suggests that there is room for improvement in the force-field description of hydrogen bonds in most modern force fields. Our results show that with current force fields, simulations beyond hundreds of nanoseconds run an increased risk of undergoing transitions to nonnative conformational states or will persist within states of high free energy for too long, thus skewing the obtained population frequencies. Only for the AMBER99sb force field have such transitions not been observed. Thus, our results have significance for the interpretation of data obtained with long MD simulations, for the selection of force fields for MD studies and for force-field development. We hope that this comprehensive benchmark based on NMR data applied to many popular MD force fields will serve as a useful resource to the MD community. Finally, we find that for gb3, the force-field AMBER99sb reaches comparable accuracy in back-calculated residual dipolar couplings and J-couplings across hydrogen bonds to ensembles obtained by refinement against NMR data.},
	number = {2},
	urldate = {2016-10-06},
	journal = {Biophys J},
	author = {Lange, Oliver F. and van der Spoel, David and de Groot, Bert L.},
	month = jul,
	year = {2010},
	pmid = {20643085},
	pmcid = {PMC2905107},
	pages = {647--655},
	file = {PubMed Central Full Text PDF:files/14/Lange et al. - 2010 - Scrutinizing Molecular Mechanics Force Fields on t.pdf:application/pdf}
}
@article{ewen_comparison_2016,
	title = {A {Comparison} of {Classical} {Force}-{Fields} for {Molecular} {Dynamics} {Simulations} of {Lubricants}},
	volume = {9},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	url = {http://www.mdpi.com/1996-1944/9/8/651},
	doi = {10.3390/ma9080651},
	abstract = {For the successful development and application of lubricants, a full understanding of their complex nanoscale behavior under a wide range of external conditions is required, but this is difficult to obtain experimentally. Nonequilibrium molecular dynamics (NEMD) simulations can be used to yield unique insights into the atomic-scale structure and friction of lubricants and additives; however, the accuracy of the results depend on the chosen force-field. In this study, we demonstrate that the use of an accurate, all-atom force-field is critical in order to; (i) accurately predict important properties of long-chain, linear molecules; and (ii) reproduce experimental friction behavior of multi-component tribological systems. In particular, we focus on n-hexadecane, an important model lubricant with a wide range of industrial applications. Moreover, simulating conditions common in tribological systems, i.e., high temperatures and pressures (HTHP), allows the limits of the selected force-fields to be tested. In the first section, a large number of united-atom and all-atom force-fields are benchmarked in terms of their density and viscosity prediction accuracy of n-hexadecane using equilibrium molecular dynamics (EMD) simulations at ambient and HTHP conditions. Whilst united-atom force-fields accurately reproduce experimental density, the viscosity is significantly under-predicted compared to all-atom force-fields and experiments. Moreover, some all-atom force-fields yield elevated melting points, leading to significant overestimation of both the density and viscosity. In the second section, the most accurate united-atom and all-atom force-field are compared in confined NEMD simulations which probe the structure and friction of stearic acid adsorbed on iron oxide and separated by a thin layer of n-hexadecane. The united-atom force-field provides an accurate representation of the structure of the confined stearic acid film; however, friction coefficients are consistently under-predicted and the friction-coverage and friction-velocity behavior deviates from that observed using all-atom force-fields and experimentally. This has important implications regarding force-field selection for NEMD simulations of systems containing long-chain, linear molecules; specifically, it is recommended that accurate all-atom potentials, such as L-OPLS-AA, are employed.},
	language = {en},
	number = {8},
	urldate = {2017-03-09},
	journal = {Materials},
	author = {Ewen, James P. and Gattinoni, Chiara and Thakkar, Foram M. and Morgan, Neal and Spikes, Hugh A. and Dini, Daniele},
	month = aug,
	year = {2016},
	keywords = {force-fields, lubricants, Molecular dynamics, tribology},
	pages = {651},
	file = {Full Text PDF:files/260/Ewen et al. - 2016 - A Comparison of Classical Force-Fields for Molecul.pdf:application/pdf;Snapshot:files/261/651.html:text/html}
}

@article{petrov_are_2014,
	title = {Are {Current} {Atomistic} {Force} {Fields} {Accurate} {Enough} to {Study} {Proteins} in {Crowded} {Environments}?},
	volume = {10},
	issn = {1553-7358},
	url = {http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003638},
	doi = {10.1371/journal.pcbi.1003638},
	abstract = {Author Summary Protein behavior is strongly affected by highly crowded and interaction-rich environments, i.e., typical conditions in both biologically relevant systems, such as the cellular interior, and solution-based structural experiments, including NMR and different spectroscopies. On the other hand, primarily because of limited computational power, molecular dynamics (MD) simulations, a premier high-resolution method for analyzing structure, dynamics and interactions of proteins, have been predominantly used to study individual proteins at infinite dilution. To fill this gap, we use MD simulations to study the behavior of wild-type (aggregation-resistant) and oxidatively damaged (aggregation-prone) forms of villin headpiece at high concentration, and reveal unexpected limitations and inaccuracies of modern-day MD force fields when it comes to modeling proteins at physiologically or experimentally relevant concentrations.},
	number = {5},
	urldate = {2017-03-09},
	journal = {PLOS Computational Biology},
	author = {Petrov, Drazen and Zagrovic, Bojan},
	month = may,
	year = {2014},
	keywords = {Biochemical simulations, Electrostatics, Intermolecular forces, Molecular dynamics, Polypeptides, Potential energy, Protein-solvent interactions, Simulation and modeling},
	pages = {e1003638},
	file = {Full Text PDF:files/265/Petrov and Zagrovic - 2014 - Are Current Atomistic Force Fields Accurate Enough.pdf:application/pdf;Snapshot:files/266/article.html:text/html}
}

@article{guvench_comparison_2008,
	title = {Comparison of protein force fields for molecular dynamics simulations},
	volume = {443},
	issn = {1064-3745},
	doi = {10.1007/978-1-59745-177-2_4},
	abstract = {In the context of molecular dynamics simulations of proteins, the term "force field" refers to the combination of a mathematical formula and associated parameters that are used to describe the energy of the protein as a function of its atomic coordinates. In this review, we describe the functional forms and parameterization protocols of the widely used biomolecular force fields Amber, CHARMM, GROMOS, and OPLS-AA. We also summarize the ability of various readily available noncommercial molecular dynamics packages to perform simulations using these force fields, as well as to use modern methods for the generation of constant-temperature, constant-pressure ensembles and to treat long-range interactions. Finally, we finish with a discussion of the ability of these force fields to support the modeling of proteins in conjunction with nucleic acids, lipids, carbohydrates, and/or small molecules.},
	language = {eng},
	journal = {Methods Mol. Biol.},
	author = {Guvench, Olgun and MacKerell, Alexander D.},
	year = {2008},
	pmid = {18446282},
	keywords = {Carbohydrates, Computer Simulation, Lipids, Nucleic Acids, Protein Conformation, Protein Folding, Proteins, Software, Temperature},
	pages = {63--88}
}

@article{villin,
	title = {Using massively parallel simulation and {Markovian} models to study protein folding: {Examining} the dynamics of the villin headpiece},
	volume = {124},
	issn = {0021-9606, 1089-7690},
	shorttitle = {Using massively parallel simulation and {Markovian} models to study protein folding},
	url = {http://scitation.aip.org/content/aip/journal/jcp/124/16/10.1063/1.2186317},
	doi = {10.1063/1.2186317},
	abstract = {We report on the use of large-scale distributed computing simulation and novel analysis techniques for examining the dynamics of a small protein. Matters addressed include folding rate, very long time scale kinetics, ensemble properties, and interaction with water. The target system for the study, the villin headpiece, has been of great interest to experimentalists and theorists both. Sampling totaled nearly 500 μ s —the most extensive published to date for a system of villin’s size in explicit solvent with all atom detail—and was in the form of tens of thousands of independent molecular dynamics trajectories, each several tens of nanoseconds in length. We report on kinetics sensitivity analyses that, using a set of short simulations, probed the role of water in villin’s folding and sensitivity to the simulation’s electrostatics treatment. By constructing Markovian state models (MSMs) from the collected data, we were able to propagate dynamics to times far beyond those directly simulated and to rapidly compute mean first passage times, long time kinetics (tens of microseconds), and evolution of ensemble property distributions over long times, otherwise currently impossible. We also tested our MSM by using it to predict the structure of villin de novo.},
	number = {16},
	urldate = {2016-10-06},
	journal = {J Chem Phys},
	author = {Jayachandran, Guha and Vishal, V. and Pande, Vijay S.},
	month = apr,
	year = {2006},
	keywords = {Conformational dynamics, Molecular dynamics, Proteins, Solvents, Trajectory models},
	pages = {164902},
	file = {Full Text PDF:files/10/Jayachandran et al. - 2006 - Using massively parallel simulation and Markovian .pdf:application/pdf;Snapshot:files/11/1.html:text/html}
}

@article{transferability1,
	title = {Assessment of the {Transferability} of a {Protein} {Force} {Field} for the {Simulation} of {Peptide}-{Surface} {Interactions}},
	volume = {26},
	issn = {0743-7463},
	url = {http://dx.doi.org/10.1021/la904415d},
	doi = {10.1021/la904415d},
	abstract = {In order to evaluate the transferability of existing empirical force fields for all-atom molecular simulations of protein adsorption behavior, we have developed and applied a method to calculate the adsorption free energy (ΔGads) of model peptides on functionalized surfaces for comparison with available experimental data. Simulations were conducted using the CHARMM program and force field using a host−guest peptide with the sequence TGTG-X-GTGT (where G and T are glycine and threonine amino acid residues, respectively, with X representing valine, threonine, aspartic acid, phenylalanine or lysine) over nine different functionalized alkanethiol self-assembled monolayer (SAM) surfaces with explicitly represented solvent. ΔGads was calculated using biased-energy replica exchange molecular dynamics to adequately sample the conformational states of the system. The simulation results showed that the CHARMM force-field was able to represent ΔGads within 1 kcal/mol of the experimental values for most systems, while deviations as large as 4 kcal/mol were found for others. In particular, the simulations reveal that CHARMM underestimates the strength of adsorption on the hydrophobic and positively charged amine surfaces. These results clearly show that improvements in force field parameterization are needed in order to accurately represent interactions between amino acid residues and functional groups of a surface and they provide a means for force field evaluation and modification for the eventual development and validation of an interfacial force field for the accurate simulation of protein adsorption behavior.},
	number = {10},
	urldate = {2016-10-06},
	journal = {Langmuir},
	author = {Vellore, Nadeem A. and Yancey, Jeremy A. and Collier, Galen and Latour, Robert A. and Stuart, Steven J.},
	month = may,
	year = {2010},
	pages = {7396--7404},
	file = {ACS Full Text PDF w/ Links:files/19/Vellore et al. - 2010 - Assessment of the Transferability of a Protein For.pdf:application/pdf;ACS Full Text Snapshot:files/24/la904415d.html:text/html}
}

@book{transferability2,
	title = {Biological {Interactions} on {Materials} {Surfaces}: {Understanding} and {Controlling} {Protein}, {Cell}, and {Tissue} {Responses}},
	isbn = {978-0-387-98161-1},
	shorttitle = {Biological {Interactions} on {Materials} {Surfaces}},
	abstract = {Success or failure of biomaterials, whether tissue engineered constructs, joint and dental implants, vascular grafts, or heart valves, depends on molecular-level events that determine subsequent responses of cells and tissues. This book presents the latest developments and state-of-the-art knowledge regarding protein, cell, and tissue interactions with both conventional and nanophase materials. Insight into these biomaterial surface interactions will play a critical role in further developments in fields such as tissue engineering, regenerative medicine, and biocompatibility of implanted materials and devices. With chapters written by leaders in their respective fields, this compendium will be the authoritative source of information for scientists, engineers, and medical researchers seeking not only to understand but also to control tissue-biomaterial interactions.},
	language = {en},
	publisher = {Springer Science \& Business Media},
	author = {Puleo, David A. and Bizios, Rena},
        notes = NOOPnotes,
        month = jun,
	year = {2009},
	pages = {77--78},
	keywords = {Medical / Research, Science / Life Sciences / Biophysics, Science / Life Sciences / Cell Biology, Science / Life Sciences / Molecular Biology, Technology \& Engineering / Biomedical, Technology \& Engineering / Engineering (General), Technology \& Engineering / Manufacturing, Technology \& Engineering / Materials Science}
}

@article{transferability3,
	title = {On the {Transferability} of {Force} {Field} {ParametersWith} an ab {Initio} {Force} {Field} {Developed} for {Sulfonamides}},
	volume = {107},
	issn = {1089-5639},
	url = {http://dx.doi.org/10.1021/jp026612i},
	doi = {10.1021/jp026612i},
	abstract = {With 25 organic molecules that represent popular functional groups, we tested the transferability of force field parameters using both parametrized force fields CHARMM, CFF, and MMFF and generic force fields DREIDING and UNIVERSAL. We found that, if transferred parameters are used in a parametrized force field, the calculation quality is no longer superior to that of a generic force field. To achieve high quality in predictions, new parameters should be created from ab initio data whenever necessary. We investigated this approach and found that a custom-built force field can be made to reproduce ab initio results if parameters are derived specifically for the molecules of interest. The parametrization procedure was applied to a group of classic antibacterial drug molecules, the sulfonamides.},
	number = {2},
	urldate = {2016-10-06},
	journal = {J. Phys. Chem. A},
	author = {Sato, F. and Hojo, S. and Sun, H.},
	month = jan,
	year = {2003},
	pages = {248--257},
	file = {ACS Full Text PDF w/ Links:files/26/Sato et al. - 2003 - On the Transferability of Force Field ParametersWi.pdf:application/pdf;ACS Full Text Snapshot:files/27/jp026612i.html:text/html}
}

@article{transferability4,
	title = {Transferable force fields for adsorption of small gases in zeolites},
	volume = {17},
	issn = {1463-9084},
	doi = {10.1039/c5cp03749b},
	abstract = {We provide transferable force fields for oxygen, nitrogen, and carbon monoxide that are able to reproduce experimental adsorption in both pure silica and alumino-substituted zeolites at cryogenic and high temperatures. The force field parameters can be combined with those previously reported for carbon dioxide, methane, and argon, opening the possibility for studying mixtures of interest containing the six components. Using these force field parameters we obtained some adsorption isotherms at cryogenic temperatures that at first sight were in discrepancies with experimental values for certain molecules and structures. We attribute these discrepancies to the sensitiveness of the equipment and to kinetic impedimenta that can lead to erratic results. Additional problems can be found during simulations when extra-framework cations are present in the system as their lack of mobility at low temperatures could lead to kinetic effects that hinder experimental adsorption.},
	language = {eng},
	number = {37},
	journal = {Phys Chem Chem Phys},
	author = {Martin-Calvo, A. and Guti{\'e}rrez-Sevillano, J. J. and Parra, J. B. and Ania, C. O. and Calero, S.},
	month = oct,
	year = {2015},
	pmid = {26313242},
	pages = {24048--24055}
}

@article{GAAMP,
	title = {Automated {Force} {Field} {Parameterization} for {Nonpolarizable} and {Polarizable} {Atomic} {Models} {Based} on {Ab} {Initio} {Target} {Data}},
	volume = {9},
	issn = {1549-9618},
	url = {http://dx.doi.org/10.1021/ct4003477},
	doi = {10.1021/ct4003477},
	abstract = {Classical molecular dynamics (MD) simulations based on atomistic models are increasingly used to study a wide range of biological systems. A prerequisite for meaningful results from such simulations is an accurate molecular mechanical force field. Most biomolecular simulations are currently based on the widely used AMBER and CHARMM force fields, which were parametrized and optimized to cover a small set of basic compounds corresponding to the natural amino acids and nucleic acid bases. Atomic models of additional compounds are commonly generated by analogy to the parameter set of a given force field. While this procedure yields models that are internally consistent, the accuracy of the resulting models can be limited. In this work, we propose a method, general automated atomic model parameterization (GAAMP), for generating automatically the parameters of atomic models of small molecules using the results from ab initio quantum mechanical (QM) calculations as target data. Force fields that were previously developed for a wide range of model compounds serve as initial guesses, although any of the final parameter can be optimized. The electrostatic parameters (partial charges, polarizabilities, and shielding) are optimized on the basis of QM electrostatic potential (ESP) and, if applicable, the interaction energies between the compound and water molecules. The soft dihedrals are automatically identified and parametrized by targeting QM dihedral scans as well as the energies of stable conformers. To validate the approach, the solvation free energy is calculated for more than 200 small molecules and MD simulations of three different proteins are carried out.},
	number = {8},
	urldate = {2016-10-07},
	journal = {J. Chem. Theory Comput.},
	author = {Huang, Lei and Roux, Benoît},
	month = aug,
	year = {2013},
	pages = {3543--3556},
	file = {ACS Full Text PDF w/ Links:files/30/Huang and Roux - 2013 - Automated Force Field Parameterization for Nonpola.pdf:application/pdf;ACS Full Text Snapshot:files/31/ct4003477.html:text/html}
}

@article{FB1,
	title = {Building {Force} {Fields}: {An} {Automatic}, {Systematic}, and {Reproducible} {Approach}},
	volume = {5},
	issn = {1948-7185},
	shorttitle = {Building {Force} {Fields}},
	url = {http://dx.doi.org/10.1021/jz500737m},
	doi = {10.1021/jz500737m},
	abstract = {The development of accurate molecular mechanics force fields is a significant challenge that must be addressed for the continued success of molecular simulation. We developed the ForceBalance method to automatically derive accurate force field parameters using flexible combinations of experimental and theoretical reference data. The method is demonstrated in the parametrization of two rigid water models, yielding new parameter sets (TIP3P-FB and TIP4P-FB) that accurately describe many physical properties of water.},
	number = {11},
	urldate = {2016-10-07},
	journal = {J. Phys. Chem. Lett.},
	author = {Wang, Lee-Ping and Martinez, Todd J. and Pande, Vijay S.},
	month = jun,
	year = {2014},
	pages = {1885--1891},
	file = {ACS Full Text PDF w/ Links:files/33/Wang et al. - 2014 - Building Force Fields An Automatic, Systematic, a.pdf:application/pdf;ACS Full Text Snapshot:files/34/jz500737m.html:text/html}
}

@article{FB2,
	title = {Systematic {Improvement} of a {Classical} {Molecular} {Model} of {Water}},
	volume = {117},
	issn = {1520-6106},
	url = {http://dx.doi.org/10.1021/jp403802c},
	doi = {10.1021/jp403802c},
	abstract = {We report the iAMOEBA (“inexpensive AMOEBA”) classical polarizable water model. The iAMOEBA model uses a direct approximation to describe electronic polarizability, in which the induced dipoles are determined directly from the permanent multipole electric fields and do not interact with one another. The direct approximation reduces the computational cost relative to a fully self-consistent polarizable model such as AMOEBA. The model is parameterized using ForceBalance, a systematic optimization method that simultaneously utilizes training data from experimental measurements and high-level ab initio calculations. We show that iAMOEBA is a highly accurate model for water in the solid, liquid, and gas phases, with the ability to fully capture the effects of electronic polarization and predict a comprehensive set of water properties beyond the training data set including the phase diagram. The increased accuracy of iAMOEBA over the fully polarizable AMOEBA model demonstrates ForceBalance as a method that allows the researcher to systematically improve empirical models by efficiently utilizing the available data.},
	number = {34},
	urldate = {2016-10-07},
	journal = {J. Phys. Chem. B},
	author = {Wang, Lee-Ping and Head-Gordon, Teresa and Ponder, Jay W. and Ren, Pengyu and Chodera, John D. and Eastman, Peter K. and Martinez, Todd J. and Pande, Vijay S.},
	month = aug,
	year = {2013},
	pages = {9956--9972},
	file = {ACS Full Text PDF w/ Links:files/41/Wang et al. - 2013 - Systematic Improvement of a Classical Molecular Mo.pdf:application/pdf;ACS Full Text Snapshot:files/43/jp403802c.html:text/html}
}

@article{FB3,
	title = {Systematic {Parametrization} of {Polarizable} {Force} {Fields} from {Quantum} {Chemistry} {Data}},
	volume = {9},
	issn = {1549-9618},
	url = {http://dx.doi.org/10.1021/ct300826t},
	doi = {10.1021/ct300826t},
	abstract = {We introduce ForceBalance, a method and free software package for systematic force field optimization with the ability to parametrize a wide variety of functional forms using flexible combinations of reference data. We outline several important challenges in force field development and how they are addressed in ForceBalance, and present an example calculation where these methods are applied to develop a highly accurate polarizable water model. ForceBalance is available for free download at https://simtk.org/home/forcebalance.},
	number = {1},
	urldate = {2016-10-07},
	journal = {J. Chem. Theory Comput.},
	author = {Wang, Lee-Ping and Chen, Jiahao and Van Voorhis, Troy},
	month = jan,
	year = {2013},
	pages = {452--460},
	file = {ACS Full Text PDF w/ Links:files/39/Wang et al. - 2013 - Systematic Parametrization of Polarizable Force Fi.pdf:application/pdf;ACS Full Text Snapshot:files/42/ct300826t.html:text/html}
}
@article{charmm2,
	title = {All-{Atom} {Empirical} {Potential} for {Molecular} {Modeling} and {Dynamics} {Studies} of {Proteins}},
	volume = {102},
	issn = {1520-6106},
	url = {http://dx.doi.org/10.1021/jp973084f},
	doi = {10.1021/jp973084f},
	abstract = {New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent−solvent, solvent−solute, and solute−solute interactions. Optimization of the internal parameters used experimental gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes between water and model compounds that represented the backbone and the various side chains. In addition, dipole moments, experimental heats and free energies of vaporization, solvation and sublimation, molecular volumes, and crystal pressures and structures were used in the optimization. The resulting protein parameters were tested by applying them to noncyclic tripeptide crystals, cyclic peptide crystals, and the proteins crambin, bovine pancreatic trypsin inhibitor, and carbonmonoxy myoglobin in vacuo and in crystals. A detailed analysis of the relationship between the alanine dipeptide potential energy surface and calculated protein φ, χ angles was made and used in optimizing the peptide group torsional parameters. The results demonstrate that use of ab initio structural and energetic data by themselves are not sufficient to obtain an adequate backbone representation for peptides and proteins in solution and in crystals. Extensive comparisons between molecular dynamics simulations and experimental data for polypeptides and proteins were performed for both structural and dynamic properties. Energy minimization and dynamics simulations for crystals demonstrate that the latter are needed to obtain meaningful comparisons with experimental crystal structures. The presented parameters, in combination with the previously published CHARMM all-atom parameters for nucleic acids and lipids, provide a consistent set for condensed-phase simulations of a wide variety of molecules of biological interest.},
	number = {18},
	urldate = {2016-10-08},
	journal = {J. Phys. Chem. B},
	author = {MacKerell, A. D. and Bashford, D. and Bellott, M. and Dunbrack, R. L. and Evanseck, J. D. and Field, M. J. and Fischer, S. and Gao, J. and Guo, H. and Ha, S. and Joseph-McCarthy, D. and Kuchnir, L. and Kuczera, K. and Lau, F. T. K. and Mattos, C. and Michnick, S. and Ngo, T. and Nguyen, D. T. and Prodhom, B. and Reiher, W. E. and Roux, B. and Schlenkrich, M. and Smith, J. C. and Stote, R. and Straub, J. and Watanabe, M. and Wiórkiewicz-Kuczera, J. and Yin, D. and Karplus, M.},
	month = apr,
	year = {1998},
	pages = {3586--3616},
	file = {ACS Full Text PDF w/ Links:files/63/MacKerell et al. - 1998 - All-Atom Empirical Potential for Molecular Modelin.pdf:application/pdf;ACS Full Text Snapshot:files/64/jp973084f.html:text/html}
}

@article{charmm1,
	title = {{CHARMM}: {A} program for macromolecular energy, minimization, and dynamics calculations},
	volume = {4},
	issn = {1096-987X},
	shorttitle = {{CHARMM}},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/jcc.540040211/abstract},
	doi = {10.1002/jcc.540040211},
	abstract = {CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a highly flexible computer program which uses empirical energy functions to model macromolecular systems. The program can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations. The operations that CHARMM can perform are described, and some implementation details are given. A set of parameters for the empirical energy function and a sample run are included.},
	language = {en},
	number = {2},
	urldate = {2016-10-08},
	journal = {J. Comput. Chem.},
	author = {Brooks, Bernard R. and Bruccoleri, Robert E. and Olafson, Barry D. and States, David J. and Swaminathan, S. and Karplus, Martin},
	month = jun,
	year = {1983},
	pages = {187--217},
	file = {Snapshot:files/58/abstract.html:text/html}
}

@article{amber,
	title = {Development and testing of a general amber force field},
	volume = {25},
	issn = {1096-987X},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/jcc.20035/abstract},
	doi = {10.1002/jcc.20035},
	abstract = {We describe here a general Amber force field (GAFF) for organic molecules. GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P, and halogens. It uses a simple functional form and a limited number of atom types, but incorporates both empirical and heuristic models to estimate force constants and partial atomic charges. The performance of GAFF in test cases is encouraging. In test I, 74 crystallographic structures were compared to GAFF minimized structures, with a root-mean-square displacement of 0.26 Å, which is comparable to that of the Tripos 5.2 force field (0.25 Å) and better than those of MMFF 94 and CHARMm (0.47 and 0.44 Å, respectively). In test II, gas phase minimizations were performed on 22 nucleic acid base pairs, and the minimized structures and intermolecular energies were compared to MP2/6-31G* results. The RMS of displacements and relative energies were 0.25 Å and 1.2 kcal/mol, respectively. These data are comparable to results from Parm99/RESP (0.16 Å and 1.18 kcal/mol, respectively), which were parameterized to these base pairs. Test III looked at the relative energies of 71 conformational pairs that were used in development of the Parm99 force field. The RMS error in relative energies (compared to experiment) is about 0.5 kcal/mol. GAFF can be applied to wide range of molecules in an automatic fashion, making it suitable for rational drug design and database searching. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1157–1174, 2004},
	language = {en},
	number = {9},
	urldate = {2016-10-08},
	journal = {J. Comput. Chem.},
	author = {Wang, Junmei and Wolf, Romain M. and Caldwell, James W. and Kollman, Peter A. and Case, David A.},
	month = jul,
	year = {2004},
	keywords = {additive force field, force field parameterization, general AMBER force field, restrained electrostatic potential (RESP)},
	pages = {1157--1174},
	file = {Full Text PDF:files/60/Wang et al. - 2004 - Development and testing of a general amber force f.pdf:application/pdf;Snapshot:files/61/abstract.html:text/html}
}

@article{mm2,
	title = {Development of a molecular mechanics ({MM}2) force field for α-chlorosilanes},
	volume = {46},
	issn = {0040-4020},
	url = {http://www.sciencedirect.com/science/article/pii/S0040402001814575},
	doi = {10.1016/S0040-4020(01)81457-5},
	abstract = {Molecular mechanics (MM2) parameters for silanes which have a Si-C-Cl fragment have been developed based on available experimental data and ab initio molecular orbital (MO) calculations. Molecular properties, mainly rotational barriers and geometries, of α-chlorosilanes have been studied using our new MM2 parameter set. Changes in the Si-C bond lengths and several bond angles of α-chlorosilanes due to the additional attachment of polar atom(s) have been investigated utilizing ab initio calculations. An electronegativity correction to both bond lengths and angles helps MM2 to reproduce results from ab initio calculations. The new force field has been applied to the conformational analysis of l-(chloromethyl)-1,2-dimethylsilacyclopentane, a model used in our studies of rearrangements of α-halosilanes.},
	number = {24},
	urldate = {2016-10-08},
	journal = {Tetrahedron},
	author = {Soo, Gyeong Cho and Cartledge, Frank K. and J. Unwalla, Rayomand and Profeta, Salvatore},
	month = jan,
	year = {1990},
	pages = {8005--8018},
	file = {ScienceDirect Snapshot:files/69/S0040402001814575.html:text/html}
}

@article{unchanged,
	title = {Force fields for protein simulations},
	volume = {66},
	issn = {0065-3233},
	language = {eng},
	journal = {Adv. Protein Chem.},
	author = {Ponder, Jay W. and Case, David A.},
	year = {2003},
	pmid = {14631816},
	keywords = {Computer Simulation, Databases, Protein, Models, Chemical, Models, Molecular, Models, Statistical, Peptides, Poisson Distribution, Protein Conformation, Protein Folding, Proteins, Static Electricity, Thermodynamics, Water},
	pages = {27--85}
}

@article{mmff,
	title = {Merck molecular force field. {I}. {Basis}, form, scope, parameterization, and performance of {MMFF}94},
	volume = {17},
	issn = {1096-987X},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1096-987X(199604)17:5/6<490::AID-JCC1>3.0.CO;2-P/abstract},
	doi = {10.1002/(SICI)1096-987X(199604)17:5/6<490::AID-JCC1>3.0.CO;2-P},
	abstract = {This article introduces MMFF94, the initial published version of the Merck molecular force field (MMFF). It describes the objectives set for MMFF, the form it takes, and the range of systems to which it applies. This study also outlines the methodology employed in parameterizing MMFF94 and summarizes its performance in reproducing computational and experimental data. Though similar to MM3 in some respects, MMFF94 differs in ways intended to facilitate application to condensed-phase processes in molecular-dynamics simulations. Indeed, MMFF94 seeks to achieve MM3-like accuracy for small molecules in a combined “organic/protein” force field that is equally applicable to proteins and other systems of biological significance. A second distinguishing feature is that the core portion of MMFF94 has primarily been derived from high-quality computational data—ca. 500 molecular structures optimized at the HF/6-31G* level, 475 structures optimized at the MP2/6-31G* level, 380 MP2/6-31G* structures evaluated at a defined approximation to the MP4SDQ/TZP level, and 1450 structures partly derived from MP2/6-31G* geometries and evaluated at the MP2/TZP level. A third distinguishing feature is that MMFF94 has been parameterized for a wide variety of chemical systems of interest to organic and medicial chemists, including many that feature frequently occurring combinations of functional groups for which little, if any, useful experimental data are available. The methodology used in parameterizing MMFF94 represents a fourth distinguishing feature. Rather than using the common “functional group” approach, nearly all MMFF parameters have been determined in a mutually consistent fashion from the full set of available computational data. MMFF94 reproduces the computational data used in its parameterization very well. In addition, MMFF94 reproduces experimental bond lengths (0.014 Å root mean square [rms]), bond angles (1.2° rms), vibrational frequencies (61 cm−1 rms), conformational energies (0.38 kcal/mol/rms), and rotational barriers (0.39 kcal/mol rms) very nearly as well as does MM3 for comparable systems. MMFF94 also describes intermolecular interactions in hydrogen-bonded systems in a way that closely parallels that given by the highly regarded OPLS force field. © 1996 John Wiley \& Sons, Inc.},
	language = {en},
	number = {5-6},
	urldate = {2016-10-08},
	journal = {J. Comput. Chem.},
	author = {Halgren, Thomas A.},
	month = apr,
	year = {1996},
	pages = {490--519},
	file = {Full Text PDF:files/66/Halgren - 1996 - Merck molecular force field. I. Basis, form, scope.pdf:application/pdf;Snapshot:files/67/abstract.html:text/html}
}

@article{parm94,
	title = {A {Second} {Generation} {Force} {Field} for the {Simulation} of {Proteins}, {Nucleic} {Acids}, and {Organic} {Molecules}},
	volume = {117},
	issn = {0002-7863},
	url = {http://dx.doi.org/10.1021/ja00124a002},
	doi = {10.1021/ja00124a002},
	number = {19},
	urldate = {2016-10-09},
	journal = {J. Am. Chem. Soc.},
	author = {Cornell, Wendy D. and Cieplak, Piotr and Bayly, Christopher I. and Gould, Ian R. and Merz, Kenneth M. and Ferguson, David M. and Spellmeyer, David C. and Fox, Thomas and Caldwell, James W. and Kollman, Peter A.},
	month = may,
	year = {1995},
	pages = {5179--5197},
	file = {ACS Full Text PDF w/ Links:files/76/Cornell et al. - 1995 - A Second Generation Force Field for the Simulation.pdf:application/pdf;ACS Full Text Snapshot:files/77/ja00124a002.html:text/html}
}

@article{tip4pew,
	title = {Development of an improved four-site water model for biomolecular simulations: {TIP}4P-{Ew}},
	volume = {120},
	issn = {0021-9606, 1089-7690},
	shorttitle = {Development of an improved four-site water model for biomolecular simulations},
	url = {http://scitation.aip.org/content/aip/journal/jcp/120/20/10.1063/1.1683075},
	doi = {10.1063/1.1683075},
	abstract = {A re-parameterization of the standard TIP4P water model for use with Ewald techniques is introduced, providing an overall global improvement in water properties relative to several popular nonpolarizable and polarizable water potentials. Using high precision simulations, and careful application of standard analytical corrections, we show that the new TIP4P-Ew potential has a density maximum at ∼1 °C, and reproduces experimental bulk-densities and the enthalpy of vaporization, ΔH vap , from −37.5 to 127 °C at 1 atm with an absolute average error of less than 1\%. Structural properties are in very good agreement with x-ray scattering intensities at temperatures between 0 and 77 °C and dynamical properties such as self-diffusion coefficient are in excellent agreement with experiment. The parameterization approach used can be easily generalized to rehabilitate any water force field using available experimental data over a range of thermodynamic points.},
	number = {20},
	urldate = {2016-10-09},
	journal = {The Journal of Chemical Physics},
	author = {Horn, Hans W. and Swope, William C. and Pitera, Jed W. and Madura, Jeffry D. and Dick, Thomas J. and Hura, Greg L. and Head-Gordon, Teresa},
	month = may,
	year = {2004},
	keywords = {Biomolecular structure, Enthalpy, Self diffusion, Vaporization, X-ray scattering},
	pages = {9665--9678},
	file = {Full Text PDF:files/79/Horn et al. - 2004 - Development of an improved four-site water model f.pdf:application/pdf;Snapshot:files/80/1.html:text/html}
}
"""
@article{bayes_imbalance,
	title = {A {Bayesian} {Modelling} {Approach} with {Balancing} {Informative} {Prior} for {Analysing} {Imbalanced} {Data}},
	volume = {11},
	issn = {1932-6203},
	url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0152700},
	doi = {10.1371/journal.pone.0152700},
	abstract = {When a dataset is imbalanced, the prediction of the scarcely-sampled subpopulation can be over-influenced by the population contributing to the majority of the data. The aim of this study was to develop a Bayesian modelling approach with balancing informative prior so that the influence of imbalance to the overall prediction could be minimised. The new approach was developed in order to weigh the data in favour of the smaller subset(s). The method was assessed in terms of bias and precision in predicting model parameter estimates of simulated datasets. Moreover, the method was evaluated in predicting optimal dose levels of tobramycin for various age groups in a motivating example. The bias estimates using the balancing informative prior approach were smaller than those generated using the conventional approach which was without the consideration for the imbalance in the datasets. The precision estimates were also superior. The method was further evaluated in a motivating example of optimal dosage prediction of tobramycin. The resulting predictions also agreed well with what had been reported in the literature. The proposed Bayesian balancing informative prior approach has shown a real potential to adequately weigh the data in favour of smaller subset(s) of data to generate robust prediction models.},
	number = {4},
	urldate = {2016-10-08},
	journal = {PLOS ONE},
	author = {Klein, Kerenaftali and Hennig, Stefanie and Paul, Sanjoy Ketan},
	month = apr,
	year = {2016},
	keywords = {Age distribution, Age groups, Cystic fibrosis, Dose prediction methods, Forecasting, Infants, Pediatrics, Simulation and modeling},
	pages = {e0152700},
	file = {Full Text PDF:files/47/Klein et al. - 2016 - A Bayesian Modelling Approach with Balancing Infor.pdf:application/pdf;Snapshot:files/51/article.html:text/html}
}
"""
@article{bayes_coarse,
	title = {Bayesian calibration of coarse-grained forces: {Efficiently} addressing transferability},
	volume = {144},
	issn = {0021-9606, 1089-7690},
	shorttitle = {Bayesian calibration of coarse-grained forces},
	url = {http://scitation.aip.org/content/aip/journal/jcp/144/15/10.1063/1.4945380},
	doi = {10.1063/1.4945380},
	abstract = {Generating and calibrating forces that are transferable across a range of state-points remains a challenging task in coarse-grained (CG) molecular dynamics. In this work, we present a coarse-graining workflow, inspired by ideas from uncertainty quantification and numerical analysis, to address this problem. The key idea behind our approach is to introduce a Bayesian correction algorithm that uses functional derivatives of CG simulations to rapidly and inexpensively recalibrate initial estimates f0 of forces anchored by standard methods such as force-matching. Taking density-temperature relationships as a running example, we demonstrate that this algorithm, in concert with various interpolation schemes, can be used to efficiently compute physically reasonable force curves on a fine grid of state-points. Importantly, we show that our workflow is robust to several choices available to the modeler, including the interpolation schemes and tools used to construct f0. In a related vein, we also demonstrate that our approach can speed up coarse-graining by reducing the number of atomistic simulations needed as inputs to standard methods for generating CG forces.},
	number = {15},
	urldate = {2016-10-09},
	journal = {The Journal of Chemical Physics},
	author = {Patrone, Paul N. and Rosch, Thomas W. and Jr, Frederick R. Phelan},
	month = apr,
	year = {2016},
	keywords = {Basis sets, Calibration, Interpolation, Polynomials, Probability theory},
	pages = {154101},
	file = {Full Text PDF:files/82/Patrone et al. - 2016 - Bayesian calibration of coarse-grained forces Eff.pdf:application/pdf;Snapshot:files/85/1.html:text/html}
}

@article{robustness,
	title = {Robustness in the fitting of molecular mechanics parameters},
	volume = {36},
	issn = {1096-987X},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/jcc.23897/abstract},
	doi = {10.1002/jcc.23897},
	abstract = {Automated methods for force field parametrization have attracted renewed interest of the community, but the robustness issues associated with the often ill-conditioned nature of parameter optimization have been vastly underappreciated in the recent literature. For this reason, this article offers a detailed description of the origin and nature of these issues. This includes a discussion of the restrained electrostatic potential fit (RESP) charge model, which does contain explicit robustness-enhancing measures albeit not in the context of bonded parameters, and which forms an inspiration for the present work. It is also discussed how all the bonded parameters in a Class I force field can be simultaneously fit using the linear least squares (LLS) procedure, and a novel restraining strategy is presented that overcomes robustness issues in the LLS fitting of bonded parameters while minimally impacting the fitted values of well-behaved parameters. Two variants of this methodology are then validated through a number of case studies, including the fitting of bond-charge increments, which illustrates the method's potential for robustly solving general LLS problems beyond force field parametrization. © 2015 Wiley Periodicals, Inc.},
	language = {en},
	number = {14},
	urldate = {2016-10-11},
	journal = {J. Comput. Chem.},
	author = {Vanommeslaeghe, Kenno and Yang, Mingjun and MacKerell, Alexander D.},
	month = may,
	year = {2015},
	keywords = {CHARMM, empirical force fields, linear least squares, optimization, robustness},
	pages = {1083--1101},
	file = {Full Text PDF:files/88/Vanommeslaeghe et al. - 2015 - Robustness in the fitting of molecular mechanics p.pdf:application/pdf;Snapshot:files/89/abstract.html:text/html}
}

@article{villin2,
	title = {Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments},
	volume = {108},
	issn = {1091-6490},
	doi = {10.1073/pnas.1010880108},
	abstract = {As the fastest folding protein, the villin headpiece (HP35) serves as an important bridge between simulation and experimental studies of protein folding. Despite the simplicity of this system, experiments continue to reveal a number of surprises, including structure in the unfolded state and complex equilibrium dynamics near the native state. Using 2.5 ms of molecular dynamics and Markov state models, we connect to current experimental results in three ways. First, we present and validate a novel method for the quantitative prediction of triplet-triplet energy transfer experiments. Second, we construct a many-state model for HP35 that is consistent with previous experiments. Finally, we predict contact-formation time traces for all 1,225 possible triplet-triplet energy transfer experiments on HP35.},
	language = {eng},
	number = {31},
	journal = {Proc. Natl. Acad. Sci. U.S.A.},
	author = {Beauchamp, Kyle A. and Ensign, Daniel L. and Das, Rhiju and Pande, Vijay S.},
	month = aug,
	year = {2011},
	pmid = {21768345},
	pmcid = {PMC3150881},
	keywords = {Electron Transport, Energy Transfer, Kinetics, Microfilament Proteins, Models, Chemical, Models, Molecular, Molecular Dynamics Simulation, Mutation, Protein Conformation, Protein Folding, Protein Structure, Secondary, Protein Structure, Tertiary},
	pages = {12734--12739}
}
"""
@article{mix,
	title = {Dynamic properties of water/alcohol mixtures studied by computer simulation},
	volume = {119},
	issn = {0021-9606, 1089-7690},
	url = {http://scitation.aip.org/content/aip/journal/jcp/119/14/10.1063/1.1607918},
	doi = {10.1063/1.1607918},
	abstract = {We have studied mixtures of alcohol and water in an extensive series of 465 molecular-dynamics simulations with an aggregate length of 713 ns, in order to study excess properties of mixing, in particular the relation between mobility and viscosity. Methanol/water, ethanol/water, and 1-propanol/water mixtures were simulated using an alcohol content of 0–100 mass \% in steps of 10\%, using the OPLS (optimized potential for liquid simulations) force field for the alcohol molecules and the TIP4P (transferable intermolecular potential with four particles) water model. Computed densities and energies show very good agreement with experimental data for bulk simulations and the mixtures are satisfactory as well. The shear viscosity was computed using nonequilibrium molecular-dynamics simulations. Other properties studied include diffusion constants and rotational correlation times. We find the mobility to correlate well with the viscosity data, i.e., at intermediate alcohol concentrations the viscosity is maximal and the mobility is minimal. Furthermore, we have combined the viscosity and diffusion calculations in order to compute an effective hydrodynamic radius of the particles in the mixtures, using the Stokes–Einstein relation. This analysis indicates that there is no collective diffusion of molecular clusters in these mixtures. For all properties we find that the excess values are underestimated in the simulations, which, given that the pure liquids are described rather well, raises the question whether the potential function is too simplistic to describe mixtures quantitatively. The set of simulations presented here can hence be regarded as a force-field benchmark.},
	number = {14},
	urldate = {2016-10-11},
	journal = {The Journal of Chemical Physics},
	author = {Wensink, Erik J. W. and Hoffmann, Alex C. and Maaren, Paul J. van and Spoel, David van der},
	month = oct,
	year = {2003},
	keywords = {Cluster analysis, Computer Simulation, Diffusion, Ethanol, Viscosity},
	pages = {7308--7317},
	file = {Full Text PDF:files/93/Wensink et al. - 2003 - Dynamic properties of wateralcohol mixtures studi.pdf:application/pdf;Snapshot:files/94/1.html:text/html}
}
"""
@article{mm1,
	title = {Conformational analysis. {LXIX}. {Improved} force field for the calculation of the structures and energies of hydrocarbons},
	volume = {93},
	issn = {0002-7863},
	url = {http://dx.doi.org/10.1021/ja00736a012},
	doi = {10.1021/ja00736a012},
	number = {7},
	urldate = {2016-10-14},
	journal = {J. Am. Chem. Soc.},
	author = {Allinger, Norman L. and Tribble, M. Thomas and Miller, Mary Ann and Wertz, David H.},
	month = apr,
	year = {1971},
	pages = {1637--1648},
	file = {ACS Full Text PDF:files/96/Allinger et al. - 1971 - Conformational analysis. LXIX. Improved force fiel.pdf:application/pdf;ACS Full Text Snapshot:files/97/ja00736a012.html:text/ht}
}
"""
@article{thermopyl,
	title = {Toward {Automated} {Benchmarking} of {Atomistic} {Force} {Fields}: {Neat} {Liquid} {Densities} and {Static} {Dielectric} {Constants} from the {ThermoML} {Data} {Archive}},
	volume = {119},
	issn = {1520-6106},
	shorttitle = {Toward {Automated} {Benchmarking} of {Atomistic} {Force} {Fields}},
	url = {http://dx.doi.org/10.1021/acs.jpcb.5b06703},
	doi = {10.1021/acs.jpcb.5b06703},
	abstract = {Atomistic molecular simulations are a powerful way to make quantitative predictions, but the accuracy of these predictions depends entirely on the quality of the force field employed. Although experimental measurements of fundamental physical properties offer a straightforward approach for evaluating force field quality, the bulk of this information has been tied up in formats that are not machine-readable. Compiling benchmark data sets of physical properties from non-machine-readable sources requires substantial human effort and is prone to the accumulation of human errors, hindering the development of reproducible benchmarks of force-field accuracy. Here, we examine the feasibility of benchmarking atomistic force fields against the NIST ThermoML data archive of physicochemical measurements, which aggregates thousands of experimental measurements in a portable, machine-readable, self-annotating IUPAC-standard format. As a proof of concept, we present a detailed benchmark of the generalized Amber small-molecule force field (GAFF) using the AM1-BCC charge model against experimental measurements (specifically, bulk liquid densities and static dielectric constants at ambient pressure) automatically extracted from the archive and discuss the extent of data available for use in larger scale (or continuously performed) benchmarks. The results of even this limited initial benchmark highlight a general problem with fixed-charge force fields in the representation low-dielectric environments, such as those seen in binding cavities or biological membranes.},
	number = {40},
	urldate = {2016-10-14},
	journal = {J. Phys. Chem. B},
	author = {Beauchamp, Kyle A. and Behr, Julie M. and Rustenburg, Ariën S. and Bayly, Christopher I. and Kroenlein, Kenneth and Chodera, John D.},
	month = oct,
	year = {2015},
	pages = {12912--12920}
}
"""
@article{mbar,
	title = {Statistically optimal analysis of samples from multiple equilibrium states},
	volume = {129},
	issn = {0021-9606},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2671659/},
	doi = {10.1063/1.2978177},
	abstract = {We present a new estimator for computing free energy differences and thermodynamic expectations as well as their uncertainties from samples obtained from multiple equilibrium states via either simulation or experiment. The estimator, which we call the multistate Bennett acceptance ratio estimator (MBAR) because it reduces to the Bennett acceptance ratio estimator (BAR) when only two states are considered, has significant advantages over multiple histogram reweighting methods for combining data from multiple states. It does not require the sampled energy range to be discretized to produce histograms, eliminating bias due to energy binning and significantly reducing the time complexity of computing a solution to the estimating equations in many cases. Additionally, an estimate of the statistical uncertainty is provided for all estimated quantities. In the large sample limit, MBAR is unbiased and has the lowest variance of any known estimator for making use of equilibrium data collected from multiple states. We illustrate this method by producing a highly precise estimate of the potential of mean force for a DNA hairpin system, combining data from multiple optical tweezer measurements under constant force bias.},
	number = {12},
	urldate = {2016-10-14},
	journal = {J Chem Phys},
	author = {Shirts, Michael R. and Chodera, John D.},
	month = sep,
	year = {2008},
	pmid = {19045004},
	pmcid = {PMC2671659},
	file = {PubMed Central Full Text PDF:files/103/Shirts and Chodera - 2008 - Statistically optimal analysis of samples from mul.pdf:application/pdf}
}
"""
@article{mapping,
	title = {Multistate reweighting and configuration mapping together accelerate the efficiency of thermodynamic calculations as a function of molecular geometry by orders of magnitude},
	volume = {138},
	issn = {0021-9606, 1089-7690},
	url = {http://scitation.aip.org/content/aip/journal/jcp/138/15/10.1063/1.4801332},
	doi = {10.1063/1.4801332},
	abstract = {We present an approach to calculate free energy and other thermodynamic property differences between molecules which have very little or no overlap in configuration space, but where a one-to-one mapping between the molecule geometries exists. The approach combines multistate reweighting with remapping of phase space between simulated states. We apply this method to calculate the free energy differences between non-overlapping, truncated harmonic oscillators, the free energy, enthalpy, and entropy differences between different parameterizations of rigid water, and differences in free energy of solvation between dipoles of different lengths. Previously difficult or impossible problems become either trivially easy or are improved in efficiency by two to five orders of magnitude.},
	number = {15},
	urldate = {2016-10-14},
	journal = {The Journal of Chemical Physics},
	author = {Paliwal, Himanshu and Shirts, Michael R.},
	month = apr,
	year = {2013},
	keywords = {Enthalpy, Entropy, Free energy, Free oscillations, Oscillators},
	pages = {154108},
	file = {Full Text PDF:files/105/Paliwal and Shirts - 2013 - Multistate reweighting and configuration mapping t.pdf:application/pdf;Snapshot:files/106/1.html:text/html}
}
"""

@article{GROMOS53A5,
	title = {A biomolecular force field based on the free enthalpy of hydration and solvation: {The} {GROMOS} force-field parameter sets 53A5 and 53A6},
	volume = {25},
	issn = {1096-987X},
	shorttitle = {A biomolecular force field based on the free enthalpy of hydration and solvation},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/jcc.20090/abstract},
	doi = {10.1002/jcc.20090},
	abstract = {Successive parameterizations of the GROMOS force field have been used successfully to simulate biomolecular systems over a long period of time. The continuing expansion of computational power with time makes it possible to compute ever more properties for an increasing variety of molecular systems with greater precision. This has led to recurrent parameterizations of the GROMOS force field all aimed at achieving better agreement with experimental data. Here we report the results of the latest, extensive reparameterization of the GROMOS force field. In contrast to the parameterization of other biomolecular force fields, this parameterization of the GROMOS force field is based primarily on reproducing the free enthalpies of hydration and apolar solvation for a range of compounds. This approach was chosen because the relative free enthalpy of solvation between polar and apolar environments is a key property in many biomolecular processes of interest, such as protein folding, biomolecular association, membrane formation, and transport over membranes. The newest parameter sets, 53A5 and 53A6, were optimized by first fitting to reproduce the thermodynamic properties of pure liquids of a range of small polar molecules and the solvation free enthalpies of amino acid analogs in cyclohexane (53A5). The partial charges were then adjusted to reproduce the hydration free enthalpies in water (53A6). Both parameter sets are fully documented, and the differences between these and previous parameter sets are discussed. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1656–1676, 2004},
	language = {en},
	number = {13},
	journal = {J. Comput. Chem.},
	author = {Oostenbrink, Chris and Villa, Alessandra and Mark, Alan E. and Van Gunsteren, Wilfred F.},
	month = oct,
	year = {2004},
	keywords = {force-field parameterization, free-energy calculation, GROMOS force field, hydration, solvation},
	pages = {1656--1676},
	file = {Full Text PDF:C\:\\Users\\Bryce Manubay\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\fjrkfkzw.default\\zotero\\storage\\BSDXTEP3\\Oostenbrink et al. - 2004 - A biomolecular force field based on the free entha.pdf:application/pdf;Snapshot:C\:\\Users\\Bryce Manubay\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\fjrkfkzw.default\\zotero\\storage\\W7KZ2SZQ\\abstract\;jsessionid=4A9510221179B45E17A8B34CDEC03D24.html:text/html}
}

@article{LJexpBayes,
	title = {Experimental data over quantum mechanics simulations for inferring the repulsive exponent of the {Lennard}-{Jones} potential in {Molecular} {Dynamics}},
	url = {http://arxiv.org/abs/1705.08533},
	abstract = {The Lennard-Jones (LJ) potential is a cornerstone of Molecular Dynamics (MD) simulations and among the most widely used computational kernels in science. The potential models atomistic attraction and repulsion with century old prescribed parameters (\$q=6, {\textbackslash}; p=12\$, respectively), originally related by a factor of two for simplicity of calculations. We re-examine the value of the repulsion exponent through data driven uncertainty quantification. We perform Hierarchical Bayesian inference on MD simulations of argon using experimental data of the radial distribution function (RDF) for a range of thermodynamic conditions, as well as dimer interaction energies from quantum mechanics simulations. The experimental data suggest a repulsion exponent (\$p {\textbackslash}approx 6.5\$), in contrast to the quantum simulations data that support values closer to the original (\$p=12\$) exponent. Most notably, we find that predictions of RDF, diffusion coefficient and density of argon are more accurate and robust in producing the correct argon phase around its triple point, when using the values inferred from experimental data over those from quantum mechanics simulations. The present results suggest the need for data driven recalibration of the LJ potential across MD simulations.},
	journal = {arXiv:1705.08533 [physics, stat]},
	author = {Kulakova, Lina and Arampatzis, Georgios and Angelikopoulos, Panagiotis and Chatzidoukas, Panagiotis and Papadimitriou, Costas and Koumoutsakos, Petros},
	month = may,
	year = {2017},
	note = {arXiv: 1705.08533},
	keywords = {Physics - Chemical Physics, Statistics - Applications},
	file = {arXiv\:1705.08533 PDF:C\:\\Users\\Bryce Manubay\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\fjrkfkzw.default\\zotero\\storage\\CB9PZ6JB\\Kulakova et al. - 2017 - Experimental data over quantum mechanics simulatio.pdf:application/pdf;arXiv.org Snapshot:C\:\\Users\\Bryce Manubay\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\fjrkfkzw.default\\zotero\\storage\\4UVN5HFU\\1705.html:text/html}
}

@article{UQMDrizzi,
	title = {Uncertainty {Quantification} in {MD} {Simulations}. {Part} {I}: {Forward} {Propagation}},
	volume = {10},
	issn = {1540-3459},
	shorttitle = {Uncertainty {Quantification} in {MD} {Simulations}. {Part} {I}},
	url = {http://epubs.siam.org/doi/abs/10.1137/110853169},
	doi = {10.1137/110853169},
	abstract = {This work focuses on quantifying the effect of intrinsic (thermal) noise and parametric uncertainty in molecular dynamics (MD) simulations. We consider isothermal, isobaric MD simulations of TIP4P (or four-site) water at ambient conditions, \$T=298\$ K and \$P=1\$ atm. Parametric uncertainty is assumed to originate from three force-field parameters that are parametrized in terms of standard uniform random variables. The thermal fluctuations inherent in MD simulations combine with parametric uncertainty to yield nondeterministic, noisy MD predictions of bulk water properties. Relying on polynomial chaos (PC) expansions, we develop a framework that enables us to isolate the impact of parametric uncertainty on the MD predictions and control the effect of the intrinsic noise. We construct the PC representations of quantities of interest (QoIs) using two different approaches: nonintrusive spectral projection (NISP) and Bayesian inference. We verify a priori the legitimacy of the NISP approach by verifying that the MD data satisfy regularity and smoothness conditions in the parameter space. The Bayesian inference approach relies on adaptively sampling the parameter space, based on analyzing the convergence of the PC expansions at different approximation levels. We show that for the present case, the effect of the thermal noise in the atomistic system can be controlled, and the MD predictions for the QoIs can be suitably represented using low-order PC models.},
	number = {4},
	journal = {Multiscale Model. Simul.},
	author = {Rizzi, F. and Najm, H. and Debusschere, B. and Sargsyan, K. and Salloum, M. and Adalsteinsson, H. and Knio, O.},
	month = jan,
	year = {2012},
	pages = {1428--1459},
	file = {Full Text PDF:C\:\\Users\\Bryce Manubay\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\fjrkfkzw.default\\zotero\\storage\\G6WDPXWG\\Rizzi et al. - 2012 - Uncertainty Quantification in MD Simulations. Part.pdf:application/pdf;Snapshot:C\:\\Users\\Bryce Manubay\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\fjrkfkzw.default\\zotero\\storage\\NPGDXMUN\\110853169.html:text/html}
}