Add OpenMM module

[joaomcteixeira]

The code presented in this commit was entirely done by Ivar de Leeuw during his Master course: Major Research Project (GSLS), academic year 2021-2022.

I am pushing the code after Ivar's request and in its exact original form.

In the next commits, the team will work on Ivar's code to accommodate it fully to the HADDOCK3 project.

Thanks, Ivar, for all your great work and best luck with your future studies!

[joaomcteixeira]

Made a general linting around files. Addition lint can still be done on function and variable names.

[mgiulini]

Hi @joaomcteixeira, just had a quick chat with Ivar De Leeuw about the version of the dependencies he used: it's openmm v. 7.7.0 and pdbfixer 1.8.1. I'll modify the INSTALL.md accordingly

[joaomcteixeira]

Okay. I strongly suggest having them defined as optional dependencies, same as lightdock and gdock.

[mgiulini]

Okay. I strongly suggest having them defined as optional dependencies, same as lightdock and gdock.

I totally agree.

[mgiulini]

tried a run with the example file openmm-test.cfg and commit ID #c79f47a. It's already a great work. A few "style" improvements from my user experience:

• we should clarify if the simulation uses implicit or explicit solvent at the beginning
• we should report the difference between equilibration and the actual simulation
• the logging during the actual simulation should be more frequent to allow the user to track the progress, we should inspect a bit the core openmm functions
• we could split the function runOpenMM in two or more pieces for enhancing the readability
• a warning appeared Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. probably we can safely ignore it, but I still have to check
• the integrator seed should be added as a user-defined parameter and printed during the execution, so that we could obtain (almost) identical calculations

[joaomcteixeira]

a warning appeared Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. probably we can safely ignore it, but I still have to check

I would say this is not ours and is something from openmm because we don't import from simtk. not in the original Ivar's code nor in the linted one.

[joaomcteixeira]

@mgiulini, the pre-last commit solves the globals() problem. It was not necessary because the value was the same as the key, so we can simply avoid calling the globals() dictionary.

Also corrected some defaults that were lists to single strings

[mgiulini]

As for the reproducibility: it is possible to assign a seed to the integrators, but not to the modeller functions. Therefore, the solvation boxes specified at the beginning of the simulations are bound to differ.

[rvhonorato]

lgtm

[amjjbonvin]

What will happen if a protein-ligand complex is passed to the openmm module?
Is there a check that only "pure" protein and nuclei acids are accepted?
Also I assume (did not check the openmm code) that the system is neutralised by adding counter ions. Is this true?

[VGPReys]

What will happen if a protein-ligand complex is passed to the openmm module? Is there a check that only "pure" protein and nuclei acids are accepted? Also I assume (did not check the openmm code) that the system is neutralised by adding counter ions. Is this true?

• System is neutralized
• No yet checks for ligands... must do it, good point !

[VGPReys]

• Added try/except logic to handle cases where topology cannot be generated due to unknown (by the force-field) residues.
• Also fixed module when using implicit solvent !