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absolute_submission_example.txt
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# SAMPLing challenge results for absolute free energy calculations
#
# This file will be automatically parsed. It must contain the following five sections: predictions, computational cost,
# software listing, technical details, and method description. These elements must be provided in the order shown.
#
# The data in each prediction line should be a comma-separated list of exactly 201 fields, 100 of which are optional.
# Each line must be structured as follows: system ID, F(1%), dF(1%), F(2%), dF(2%), ..., F(100%), dF(100%), where
# F(X%) and dF(X%) are respectively the free energy estimate and free energy uncertainty, both in kcal/mol, after X% of
# the calculation. The free energy uncertainties are optional (see example below).
#
# The "Prediction" section should have at least 15 lines: 5 replicates starting from the provided initial configurations
# for each of the 3 host-guest systems in the challenge (i.e., CB8-G3, OA-G3, and OA-G6). Data submission for further replicates
# or different systems is welcomed, although not required.
#
# The list of predictions must begin with the "Prediction:" keyword, as illustrated here.
Predictions:
CB8-G3-0, -9.47,, -10.72,, -9.71,, -9.89,, -9.98,, -10.41,, -10.00,, -9.54,, -9.76,, -9.86,, -9.34,, -9.80,, -9.54,, -10.17,, -9.79,, -10.32,, -9.68,, -9.64,, -9.16,, -10.01,, -10.39,, -10.59,, -10.32,, -9.31,, -10.17,, -10.41,, -10.26,, -10.23,, -9.36,, -11.26,, -9.43,, -10.35,, -9.81,, -9.71,, -9.90,, -9.05,, -9.63,, -9.68,, -9.96,, -9.43,, -8.95,, -9.47,, -10.20,, -10.82,, -10.45,, -9.51,, -9.98,, -10.06,, -10.25,, -9.81,, -10.68,, -10.34,, -9.94,, -9.74,, -10.09,, -10.18,, -10.42,, -9.77,, -8.50,, -9.79,, -9.78,, -10.64,, -10.46,, -10.06,, -9.75,, -9.71,, -9.86,, -10.26,, -9.32,, -10.11,, -9.95,, -10.11,, -10.07,, -10.50,, -10.52,, -10.48,, -10.16,, -9.23,, -9.33,, -9.73,, -10.19,, -10.25,, -9.90,, -9.68,, -10.26,, -10.03,, -10.01,, -10.23,, -10.08,, -10.23,, -10.30,, -9.81,, -9.73,, -10.65,, -9.86,, -9.91,, -9.99,, -10.38,, -10.03,, -10.57,
CB8-G3-1, -10.35,, -10.15,, -9.82,, -9.12,, -9.68,, -10.43,, -9.75,, -9.69,, -9.64,, -10.07,, -10.05,, -9.64,, -10.04,, -10.33,, -10.47,, -10.94,, -10.32,, -9.74,, -9.74,, -10.07,, -9.91,, -10.05,, -9.70,, -9.85,, -10.31,, -9.66,, -9.36,, -10.42,, -10.16,, -10.38,, -10.14,, -9.91,, -9.29,, -10.09,, -10.40,, -9.31,, -9.96,, -9.42,, -10.17,, -8.91,, -9.83,, -10.44,, -9.90,, -9.63,, -10.04,, -10.82,, -9.82,, -9.76,, -10.47,, -9.93,, -10.11,, -9.87,, -9.81,, -10.30,, -9.96,, -9.96,, -9.69,, -9.95,, -9.92,, -9.47,, -9.26,, -10.03,, -9.27,, -10.09,, -9.88,, -9.33,, -9.68,, -9.23,, -9.75,, -9.85,, -10.32,, -9.30,, -10.08,, -10.60,, -9.66,, -10.25,, -9.61,, -10.36,, -9.78,, -9.61,, -10.11,, -9.80,, -9.70,, -9.61,, -9.84,, -10.08,, -9.81,, -9.91,, -9.73,, -9.44,, -9.22,, -9.68,, -9.50,, -10.36,, -10.02,, -9.52,, -9.89,, -9.84,, -10.00,, -10.41,
CB8-G3-2, -9.63,, -10.65,, -9.92,, -9.86,, -10.80,, -10.07,, -10.71,, -10.02,, -10.93,, -10.14,, -9.39,, -10.46,, -10.35,, -10.40,, -10.82,, -10.23,, -9.62,, -10.43,, -9.23,, -10.13,, -9.72,, -9.03,, -9.40,, -10.27,, -11.02,, -9.40,, -10.14,, -9.31,, -10.10,, -10.48,, -9.34,, -9.75,, -10.19,, -9.55,, -9.75,, -9.86,, -9.85,, -10.21,, -9.52,, -10.17,, -10.68,, -10.40,, -9.81,, -9.96,, -9.66,, -10.36,, -10.05,, -9.35,, -10.32,, -9.77,, -10.47,, -10.23,, -10.48,, -9.91,, -9.90,, -9.71,, -8.97,, -10.20,, -9.59,, -11.02,, -9.17,, -10.33,, -9.86,, -10.04,, -10.33,, -10.77,, -10.12,, -9.91,, -10.30,, -10.09,, -9.73,, -9.38,, -10.77,, -10.40,, -10.27,, -9.84,, -10.64,, -9.76,, -9.65,, -10.08,, -9.13,, -9.93,, -9.58,, -10.49,, -10.08,, -10.08,, -10.81,, -9.93,, -10.25,, -10.55,, -9.97,, -10.20,, -9.70,, -10.30,, -9.99,, -9.75,, -10.26,, -10.29,, -9.82,, -9.75,
CB8-G3-3, -9.84,, -10.76,, -10.24,, -9.70,, -9.89,, -10.25,, -10.33,, -9.95,, -9.44,, -9.46,, -9.82,, -9.61,, -9.02,, -10.41,, -10.21,, -10.25,, -10.45,, -10.98,, -10.01,, -10.45,, -9.55,, -10.07,, -9.83,, -9.86,, -10.11,, -9.86,, -10.52,, -10.29,, -9.56,, -9.79,, -9.65,, -10.44,, -10.17,, -9.68,, -8.77,, -10.61,, -10.33,, -9.83,, -10.62,, -9.66,, -10.69,, -9.73,, -10.24,, -10.33,, -9.58,, -9.25,, -9.95,, -10.13,, -10.22,, -9.62,, -9.32,, -10.14,, -9.74,, -10.42,, -9.85,, -9.53,, -9.66,, -10.19,, -10.01,, -9.80,, -9.43,, -10.60,, -10.85,, -9.94,, -9.56,, -10.49,, -10.22,, -10.19,, -10.22,, -10.37,, -10.20,, -10.27,, -9.79,, -10.59,, -10.94,, -9.94,, -9.93,, -10.50,, -9.64,, -10.23,, -9.72,, -10.22,, -10.13,, -10.48,, -9.84,, -9.85,, -9.73,, -9.82,, -9.56,, -10.90,, -9.68,, -9.25,, -9.30,, -10.67,, -9.56,, -10.33,, -10.28,, -9.60,, -9.87,, -9.18,
CB8-G3-4, -10.01,, -10.02,, -10.12,, -10.19,, -9.96,, -10.41,, -10.34,, -9.92,, -10.13,, -9.36,, -9.07,, -9.37,, -10.24,, -9.59,, -10.18,, -9.40,, -9.81,, -10.12,, -10.13,, -10.14,, -9.59,, -9.47,, -10.20,, -9.98,, -9.90,, -11.26,, -10.37,, -9.67,, -10.44,, -10.64,, -10.36,, -10.56,, -9.89,, -10.38,, -8.89,, -9.98,, -9.84,, -9.84,, -10.34,, -10.06,, -10.02,, -10.01,, -9.81,, -9.32,, -9.82,, -10.41,, -9.77,, -11.34,, -9.88,, -9.44,, -10.66,, -9.70,, -10.07,, -9.35,, -9.99,, -9.55,, -9.95,, -10.93,, -9.68,, -10.15,, -10.10,, -9.68,, -9.52,, -10.36,, -9.55,, -10.20,, -9.48,, -9.71,, -9.90,, -10.53,, -9.75,, -10.09,, -9.25,, -9.84,, -9.02,, -10.04,, -9.69,, -10.10,, -10.10,, -9.84,, -10.22,, -9.57,, -9.97,, -10.07,, -10.11,, -9.68,, -9.10,, -9.85,, -10.64,, -9.23,, -10.35,, -10.30,, -10.72,, -10.12,, -9.66,, -10.03,, -10.24,, -9.27,, -10.05,, -9.85,
OA-G3-0, -14.69,, -14.80,, -14.76,, -15.00,, -15.12,, -14.78,, -14.34,, -14.83,, -15.07,, -14.98,, -15.00,, -15.52,, -14.46,, -14.95,, -15.25,, -15.26,, -15.14,, -14.67,, -15.20,, -15.31,, -15.32,, -15.92,, -15.18,, -14.98,, -15.17,, -15.35,, -15.27,, -15.13,, -14.72,, -14.89,, -14.54,, -14.16,, -15.04,, -15.12,, -14.80,, -14.75,, -14.96,, -15.19,, -14.45,, -15.09,, -14.86,, -14.78,, -14.89,, -15.41,, -15.43,, -14.98,, -15.29,, -14.88,, -14.83,, -14.05,, -15.30,, -15.05,, -14.93,, -14.80,, -15.16,, -15.13,, -14.83,, -14.68,, -15.15,, -14.57,, -15.03,, -14.63,, -15.09,, -15.58,, -14.78,, -14.91,, -15.06,, -14.63,, -15.48,, -15.48,, -15.20,, -15.05,, -15.25,, -15.19,, -14.98,, -14.69,, -15.26,, -14.92,, -14.39,, -14.90,, -15.22,, -15.04,, -14.83,, -14.68,, -14.42,, -15.57,, -14.61,, -14.50,, -14.92,, -14.92,, -15.03,, -14.82,, -14.98,, -15.27,, -15.33,, -14.84,, -14.71,, -14.87,, -14.97,, -14.45,
OA-G3-1, -15.16,, -15.21,, -15.23,, -15.04,, -15.38,, -14.98,, -14.83,, -15.15,, -14.86,, -14.76,, -15.29,, -15.01,, -14.66,, -14.77,, -14.93,, -15.03,, -14.78,, -15.14,, -14.83,, -14.77,, -15.06,, -14.96,, -14.88,, -14.69,, -14.64,, -15.22,, -14.94,, -15.34,, -14.60,, -16.07,, -15.25,, -14.96,, -15.31,, -15.21,, -14.91,, -14.82,, -14.47,, -14.61,, -15.00,, -15.29,, -14.99,, -15.18,, -14.81,, -14.72,, -15.00,, -14.90,, -14.81,, -14.64,, -15.31,, -15.02,, -14.89,, -14.69,, -14.96,, -14.57,, -15.23,, -15.70,, -15.10,, -15.04,, -14.12,, -14.93,, -15.07,, -15.04,, -14.97,, -14.92,, -14.99,, -14.44,, -15.24,, -15.41,, -15.17,, -14.94,, -15.01,, -15.00,, -14.80,, -15.58,, -14.71,, -15.36,, -15.09,, -15.06,, -15.33,, -15.19,, -14.94,, -15.16,, -15.59,, -15.50,, -14.44,, -14.92,, -15.03,, -15.18,, -14.93,, -14.68,, -15.29,, -14.62,, -15.54,, -15.22,, -14.51,, -14.72,, -14.71,, -14.66,, -14.98,, -14.25,
OA-G3-2, -14.91,, -15.56,, -15.17,, -15.04,, -14.82,, -15.08,, -15.06,, -14.05,, -14.37,, -15.34,, -15.19,, -15.13,, -14.97,, -15.41,, -14.65,, -14.73,, -14.32,, -15.09,, -14.76,, -14.97,, -14.92,, -15.23,, -15.28,, -15.11,, -15.34,, -14.73,, -14.91,, -15.24,, -15.49,, -14.43,, -15.04,, -14.72,, -14.58,, -14.40,, -15.37,, -14.97,, -15.16,, -14.70,, -14.69,, -14.54,, -14.79,, -14.56,, -14.49,, -14.81,, -15.22,, -15.49,, -15.06,, -14.51,, -15.19,, -15.47,, -14.97,, -14.41,, -14.63,, -15.31,, -15.08,, -15.51,, -14.98,, -15.19,, -14.52,, -14.90,, -15.24,, -14.64,, -15.04,, -15.31,, -14.58,, -15.56,, -14.94,, -14.62,, -14.60,, -14.86,, -14.98,, -15.12,, -15.41,, -15.38,, -14.95,, -15.02,, -14.99,, -14.52,, -14.87,, -14.71,, -14.57,, -14.76,, -14.27,, -14.26,, -14.94,, -14.97,, -14.64,, -15.23,, -14.81,, -14.72,, -14.26,, -14.78,, -14.90,, -15.06,, -14.73,, -15.16,, -14.60,, -15.48,, -14.89,, -15.06,
OA-G3-3, -14.95,, -14.66,, -15.29,, -14.80,, -14.72,, -15.25,, -15.44,, -14.73,, -15.12,, -14.72,, -14.56,, -14.52,, -14.73,, -15.23,, -14.89,, -15.22,, -14.97,, -14.56,, -14.98,, -14.79,, -14.66,, -14.74,, -15.46,, -14.89,, -15.03,, -15.00,, -15.62,, -15.23,, -14.76,, -14.84,, -15.43,, -15.32,, -14.96,, -14.80,, -15.13,, -14.54,, -14.80,, -15.09,, -14.91,, -14.94,, -14.79,, -15.14,, -15.50,, -15.31,, -15.01,, -15.03,, -15.03,, -14.90,, -14.68,, -15.33,, -14.93,, -15.03,, -15.03,, -14.77,, -14.90,, -16.05,, -15.14,, -14.78,, -14.64,, -14.72,, -14.63,, -15.16,, -15.03,, -15.08,, -14.78,, -15.09,, -14.94,, -14.43,, -15.20,, -15.00,, -15.02,, -15.46,, -15.24,, -15.10,, -14.94,, -15.20,, -15.24,, -14.82,, -14.59,, -15.33,, -14.73,, -15.48,, -14.67,, -14.93,, -14.58,, -15.45,, -15.00,, -15.29,, -15.38,, -14.59,, -14.92,, -15.01,, -14.85,, -15.16,, -14.80,, -15.39,, -14.94,, -15.21,, -14.66,, -15.00,
OA-G3-4, -14.99,, -15.22,, -15.11,, -14.69,, -15.03,, -14.91,, -15.06,, -15.34,, -15.22,, -15.22,, -15.65,, -15.22,, -14.50,, -15.58,, -15.61,, -14.86,, -15.10,, -15.03,, -14.85,, -14.91,, -14.94,, -14.62,, -15.21,, -15.14,, -14.95,, -15.25,, -15.25,, -14.78,, -14.72,, -14.91,, -14.62,, -15.08,, -14.74,, -15.27,, -15.19,, -15.20,, -14.73,, -14.73,, -15.23,, -15.17,, -15.12,, -15.45,, -15.16,, -15.08,, -14.63,, -15.11,, -15.18,, -15.24,, -15.02,, -14.92,, -15.74,, -15.03,, -14.97,, -14.94,, -15.11,, -14.97,, -15.29,, -15.69,, -15.23,, -15.12,, -14.96,, -15.26,, -14.86,, -15.03,, -15.01,, -15.47,, -15.19,, -14.49,, -15.80,, -15.09,, -14.64,, -14.45,, -15.15,, -14.52,, -15.22,, -14.59,, -14.45,, -14.48,, -15.10,, -15.70,, -14.74,, -15.44,, -14.97,, -15.14,, -14.88,, -15.26,, -14.52,, -14.79,, -14.69,, -15.29,, -14.98,, -14.52,, -15.13,, -15.31,, -15.06,, -14.68,, -15.28,, -14.49,, -14.59,, -15.09,
OA-G6-0, -2.90,, -3.70,, -2.51,, -3.56,, -3.12,, -3.65,, -2.51,, -3.80,, -2.41,, -2.83,, -2.73,, -3.50,, -3.30,, -3.87,, -2.49,, -4.74,, -2.75,, -3.49,, -1.35,, -2.82,, -3.75,, -3.11,, -2.79,, -3.02,, -3.10,, -2.48,, -1.75,, -3.75,, -4.19,, -3.53,, -3.61,, -2.24,, -2.72,, -3.34,, -4.04,, -3.41,, -3.53,, -3.32,, -2.64,, -3.15,, -2.84,, -2.66,, -2.72,, -4.04,, -3.38,, -3.47,, -2.82,, -3.45,, -4.36,, -3.55,, -3.45,, -2.27,, -2.37,, -2.27,, -3.12,, -3.61,, -2.85,, -3.02,, -2.52,, -2.31,, -2.40,, -2.79,, -0.88,, -2.08,, -3.20,, -4.20,, -3.62,, -4.34,, -3.32,, -3.22,, -1.99,, -2.29,, -3.11,, -3.35,, -2.94,, -3.57,, -1.88,, -2.65,, -3.54,, -2.60,, -3.63,, -2.57,, -3.93,, -3.13,, -2.07,, -3.22,, -2.58,, -2.80,, -3.41,, -4.12,, -2.86,, -2.54,, -3.03,, -3.06,, -3.41,, -2.40,, -2.13,, -3.17,, -3.30,, -3.54,
OA-G6-1, -3.69,, -3.11,, -2.87,, -3.39,, -2.19,, -2.89,, -4.26,, -2.48,, -4.35,, -3.23,, -3.55,, -1.49,, -1.85,, -2.90,, -2.47,, -3.13,, -3.30,, -4.25,, -2.81,, -2.82,, -2.91,, -3.58,, -2.32,, -3.40,, -4.43,, -3.13,, -3.52,, -2.12,, -2.70,, -4.30,, -3.28,, -2.76,, -3.74,, -2.79,, -2.78,, -3.22,, -3.20,, -3.08,, -3.10,, -3.10,, -1.62,, -4.19,, -2.87,, -1.80,, -2.40,, -2.65,, -1.97,, -3.53,, -3.86,, -2.90,, -3.62,, -2.62,, -3.21,, -3.55,, -2.74,, -3.91,, -2.94,, -3.44,, -3.63,, -2.60,, -2.66,, -4.33,, -3.10,, -2.84,, -3.24,, -1.83,, -2.64,, -2.52,, -3.71,, -3.39,, -2.44,, -2.27,, -3.55,, -2.34,, -2.62,, -3.53,, -3.16,, -2.71,, -3.11,, -2.51,, -3.25,, -2.61,, -2.76,, -2.98,, -3.09,, -3.11,, -3.91,, -3.62,, -3.14,, -2.33,, -2.86,, -2.83,, -3.11,, -3.24,, -3.17,, -1.94,, -4.41,, -2.65,, -2.88,, -2.06,
OA-G6-2, -2.90,, -4.15,, -3.21,, -2.64,, -4.10,, -3.42,, -1.99,, -2.25,, -3.62,, -3.79,, -3.07,, -3.68,, -3.26,, -1.23,, -3.44,, -2.94,, -2.73,, -2.51,, -3.42,, -3.95,, -3.59,, -1.44,, -3.82,, -2.02,, -2.69,, -4.08,, -2.48,, -3.02,, -2.59,, -2.89,, -3.58,, -2.65,, -3.15,, -3.03,, -4.04,, -2.90,, -2.99,, -3.58,, -2.23,, -2.40,, -2.72,, -2.86,, -4.02,, -3.39,, -3.73,, -2.19,, -2.98,, -2.65,, -3.73,, -3.18,, -1.85,, -2.47,, -4.30,, -2.84,, -2.09,, -3.00,, -3.15,, -2.78,, -2.73,, -3.56,, -3.40,, -3.44,, -3.17,, -2.52,, -3.19,, -3.58,, -3.31,, -4.45,, -3.35,, -2.31,, -2.58,, -1.87,, -2.09,, -1.97,, -3.89,, -3.57,, -2.38,, -3.85,, -3.91,, -2.70,, -3.13,, -2.84,, -1.79,, -2.66,, -3.20,, -2.70,, -3.64,, -3.04,, -3.14,, -4.01,, -3.85,, -2.50,, -2.70,, -3.25,, -3.53,, -2.41,, -2.38,, -2.98,, -2.36,, -3.41,
OA-G6-3, -1.74,, -3.79,, -2.04,, -3.33,, -2.69,, -3.02,, -3.47,, -3.45,, -3.02,, -3.46,, -2.94,, -3.68,, -2.07,, -2.97,, -3.51,, -2.85,, -3.64,, -3.21,, -3.80,, -2.77,, -3.40,, -3.13,, -2.90,, -3.63,, -3.30,, -3.19,, -3.64,, -2.12,, -4.65,, -3.52,, -3.76,, -3.41,, -3.67,, -2.89,, -3.69,, -2.64,, -2.17,, -2.89,, -2.65,, -2.37,, -4.33,, -3.11,, -3.12,, -2.75,, -2.47,, -3.97,, -2.59,, -2.40,, -3.32,, -3.06,, -3.70,, -2.08,, -3.17,, -3.62,, -2.30,, -2.61,, -2.20,, -3.66,, -3.70,, -2.71,, -2.39,, -3.68,, -3.06,, -3.33,, -4.26,, -2.41,, -2.26,, -2.84,, -3.37,, -4.05,, -2.09,, -2.13,, -3.62,, -3.02,, -4.34,, -4.28,, -3.37,, -3.54,, -3.26,, -1.52,, -2.37,, -3.49,, -3.71,, -3.72,, -2.08,, -2.68,, -3.37,, -3.63,, -2.93,, -3.01,, -2.53,, -3.05,, -4.13,, -2.36,, -2.45,, -3.96,, -2.47,, -2.95,, -2.29,, -4.09,
OA-G6-4, -3.45,, -2.74,, -3.76,, -3.52,, -3.24,, -2.23,, -3.77,, -3.35,, -2.45,, -4.36,, -2.09,, -4.23,, -3.33,, -3.84,, -2.93,, -2.99,, -1.89,, -3.24,, -2.64,, -2.94,, -3.78,, -3.06,, -2.52,, -3.17,, -2.35,, -3.66,, -2.41,, -3.34,, -2.86,, -2.07,, -4.38,, -2.28,, -4.18,, -3.77,, -2.97,, -2.36,, -3.50,, -4.24,, -2.60,, -2.49,, -3.10,, -1.98,, -3.93,, -3.49,, -2.72,, -3.47,, -2.86,, -3.42,, -2.73,, -2.67,, -2.87,, -2.57,, -2.63,, -4.20,, -2.23,, -3.33,, -2.44,, -2.92,, -3.56,, -3.18,, -2.04,, -3.05,, -2.93,, -2.62,, -3.99,, -1.28,, -1.45,, -2.38,, -1.93,, -2.82,, -2.56,, -3.02,, -3.03,, -3.40,, -3.03,, -3.27,, -2.17,, -2.98,, -2.42,, -1.47,, -2.14,, -3.37,, -2.85,, -3.39,, -3.37,, -3.49,, -3.52,, -2.49,, -2.35,, -3.88,, -3.18,, -3.24,, -3.73,, -2.57,, -2.86,, -3.43,, -3.19,, -3.72,, -3.65,, -2.84,
#
# Each line of the "Cost" section below should include the following four elements in this order: system ID, total number of energy evaluations,
# total wall-clock time (in seconds), and total CPU time (in seconds). The CPU time is optional (the example below
# does not report it). The "Cost:" keyword is required.
#
# The total number of energy evaluations should approximately be the same for all 5 replicates of each system. This
# is necessary to be able to compute meaningful performance statistics from the data in the "Predictions" section.
#
# If your implementation is distributed over multiple processes/CPUs/GPUs, please include in the "TechnicalDetails"
# section a description of the parallelization strategy that clarifies how to interpret the wall-clock time.
Cost:
CB8-G3-0, 635790000, 1176166475.3,
CB8-G3-1, 635790000, 1208422743.2,
CB8-G3-2, 635790000, 1218082320.5,
CB8-G3-3, 635790000, 1082762273.0,
CB8-G3-4, 635790000, 1268320857.7,
OA-G3-0, 768855000, 1660536157.6,
OA-G3-1, 768855000, 1613619830.4,
OA-G3-2, 768855000, 1780458468.7,
OA-G3-3, 768855000, 1588242380.8,
OA-G3-4, 768855000, 1351436969.6,
OA-G6-0, 759270000, 1574180602.7,
OA-G6-1, 759270000, 1505975557.8,
OA-G6-2, 759270000, 1677228832.9,
OA-G6-3, 759270000, 1629967035.5,
OA-G6-4, 759270000, 1437224224.2,
#
# Please provide an informal yet informative name for the method used.
# The "Name:" keyword is required, as shown here.
Name:
Langevin/HREX/MBAR
#
# All major software packages used and their versions.
# The "Software:" keyword is required.
Software:
OpenMM 7.1.1
OpenMMTools 0.13.4
YANK 0.19.4
#
# A description of the hardware used to run the simulations. If your implementation is distributed over multiple
# processes/CPUs/GPUs, please include a description of the parallelization strategy that clarifies how to interpret
# the total wall-clock time given in the "Cost" section. The "TechnicalDetails:" keyword is required.
TechnicalDetails:
All the simulations were performed on two GeForce GTX 1080 on a single machine hosting an Intel Xeon Processor E5-2697 v4.
The replicas were divided into two sets of the same size and propagated in parallel on the two GPUs, while the exchange
stage was performed serially. We estimate the total wall-clock time spent doing parallel/serial work to be
approximately 95%/5% respectively.
#
# Methodology and computational details.
# The level of detail should be at least that used in a publication. Please include the values of key parameters,
# with units, and explain how any statistical uncertainties were estimated. In particular, be sure to include a
# complete description of the thermodynamic cycle and the number of states (or windows) employed.
#
# Use as many lines of text as you need. All text following the "Method:" keyword will be regarded as part of your
# free text methods description.
Method:
The alchemical free energy calculations were performed using the Hamiltonian Replica Exchange method.
First, ligand charges were annihilated and then van der Waals were decoupled using a linear protocol
with spacing Dlambda=0.05. A total of 92 windows were used (41 for the complex and 41 for the ligand
in solution). A harmonic restraint was used in the complex phase to keep the ligand in the binding
pocket, and an analytical correction was applied to release the ligand at the standard concentration.
Each iteration of the algorithm consisted of 500 steps of Langevin dynamics (BAOAB splitting) with a 2fs
time step, followed by a replica mixing stage. The latter was performed using a Gibbs sampling scheme
attempting 6 million replica swaps every iteration. All simulations run for 15000 iterations (i.e., 15ns per replica).