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molecularmachines / moleculib

Moleculib is a python library for preparing and processing biomolecular data in machine learning pipelines.
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Dynamics: Connecting CHARMM-GUI Forcefield to OpenMM Setup #18

Open ManvithaPonnapati opened 1 year ago

ManvithaPonnapati commented 1 year ago

Figure out how to accept the force field fields from the charmm-gui

Charmm-gui files for opsin 3ug9 are here https://drive.google.com/drive/folders/1Vx2iVaYiJ5TXwPIC27XoHBRujOd97s5U?usp=drive_link

jenny-df commented 1 year ago

We can add these kinds of file types to the force fields section in OpenMM (source):

  1. .rtf, .top – Residue topology file
  2. .par, .prm – Parameter file
  3. .str – Stream file
  4. .inp – Only if “par” is in the file name, it is a parameter file

We should probably use everything in the toppar folder except for the .crd file - "tip216.crd" (source. I don't think we should include "step5_assembly.str" and "step5_input_minimization.str" since they include information about the box rather than the force field itself. There is also a file called toppar.str in the main folder that we shouldn't include. It doesn't have the correct format for a .str file (it has a line containing "read" but never has a line containing "end" for the read to stop.)

jenny-df commented 1 year ago

I was able to run a simulation with the files above on the OpenMM GUI, but I changed some of the parameter of the simulation. I set "Non-Bonded Method" to "Cutoff, non-periodic" and "Statistical Ensemble" to "Constant Volume, temperature".