Inquiry about monitoring the trajectory of attach-pull-release method.

[bowensha-tudelft]

As the title mentions, I cannot find any trajectory generated by paprika. I hope I can see the trajectory of the process so that I can be sure that the method is correctly implemented. Could you please tell me where I can look into for more details?

[jset231]

@bowensha-tudelft Can you give us more info on your code to run the simulations with paprika. Are you using Amber or OpenMM? When you say there is no trajectory, do you mean no files are generated?

[bowensha-tudelft]

@bowensha-tudelft Can you give us more info on your code to run the simulations with paprika. Are you using Amber or OpenMM? When you say there is no trajectory, do you mean no files are generated?

I am using AMBER. There are some files in complex/ and windows/. But I do not have any idea about which one contains information of trajectory.

[jset231]

@bowensha-tudelft in those folders there should be subfolders like a000, a001 for the attach phase and p000, p001 for the pull phase. These folders will contain all of the trajectories (if AMBER ran properly). Can you find these in the directory?

[bowensha-tudelft]

@bowensha-tudelft in those folders there should be subfolders like a000, a001 for the attach phase and p000, p001 for the pull phase. These folders will contain all of the trajectories (if AMBER ran properly). Can you find these in the directory?

Yes, I can find them. Above are files in it.

[jset231]

Awesome. The *.nc files are the AMBER trajectories you can load into a visualization software like VMD.

[bowensha-tudelft]

Awesome. The *.nc files are the AMBER trajectories you can load into a visualization software like VMD.

Thank you so much! AMBER is really new to me. Your suggestions are strongly useful.

[bowensha-tudelft]

Awesome. The *.nc files are the AMBER trajectories you can load into a visualization software like VMD.

Sorry, @jset231 . I am confused with loading the trajectory. Below is what I did.

File - New Molecule - Filename: bcd-hex-dum.prmtop
Load Data Into Molecule - Filename: production.nc & Determine file type: AMBER Coordinates

Nothing shows on my VMD windows but VMD gives this message:

[jaketanderson]

@bowensha-tudelft if you provide the specific prmtop and nc files here, I can try opening them on my own VMD. That could help us narrow the issue down to VMD plugin issues or issues with the files themselves.