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wiederm / endstate_correction

Endstate corrections from MM to QML potential
https://wiederm.github.io/endstate_correction/
MIT License
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About potential input files #41

Closed xiki-tempula closed 2 years ago

xiki-tempula commented 2 years ago

Hi, Thank you very much for the package. I'm very interested in this repo and wish to have a go with it. I wonder if I could have some input files to test it? Thank you.

wiederm commented 2 years ago

Hi! Sure, I will provide some input files! We are currently in the process of setting up a better documentation and HOW-TO (which should be finished after the weekend). I will point you to the improved HOW-TO-USE tutorial with some input files as soon as it is online but latest on Monday.

xiki-tempula commented 2 years ago

@wiederm Great Thanks.

wiederm commented 2 years ago

The documentation outlines now how to do an endstate correction for 1-octanol (in a waterbox) with FEP and NEQ: https://wiederm.github.io/endstate_correction/getting_started.html#a-typical-neq-workflow

xiki-tempula commented 2 years ago

Thanks for the documentation. It might be good to add the imports to the top of the code block

from openmm.app.charmmparameterset import CharmmParameterSet
from openmm.app.charmmpsffile import CharmmPsfFile
from openmm.app.pdbfile import PDBFile

And set the location of the 1-octanol explicitly so people know where to find the files

parameter_base='endstate_correction/data/jctc_data'
system_name='1_octanol'

Then from

psf = CharmmPsfFile(f"{parameter_base}/{system_name}/charmm-gui/openmm/step3_input.psf")
pdb = PDBFile(f"{parameter_base}/{system_name}/charmm-gui/openmm/step3_input.pdb")
params = CharmmParameterSet(
    f"{parameter_base}/{system_name}/charmm-gui/unk/unk.rtf",
    f"{parameter_base}/{system_name}/charmm-gui/unk/unk.prm",
    f"{parameter_base}/toppar/top_all36_cgenff.rtf",
    f"{parameter_base}/toppar/par_all36_cgenff.prm",
    f"{parameter_base}/toppar/toppar_water_ions.str",
)

I wonder how do I get ml_atoms = [atom.index for atom in chains[0].atoms()]? Thanks.