The functionality of OpenMM will (eventually) include everything that one would need to run modern molecular simulation.
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Joe Napoli
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by Joe Napoli » Mon Feb 08, 2016 2:44 pm
Hi,
I would like to simulate a small molecule with explicit solvent in OpenMM. I have created CHARMM force field files using CGenFF:
https://cgenff.paramchem.org/. My question is whether it is possible to straightforwardly solvate this molecule and simulate it using an arbitrary explicit water model (e.g. qTIP4P/f). One route that I think might work is: (1) serialize the force field using the xmlserializer in OpenMM, (2) create a force field object by loading a list of xml files, e.g.
Code: Select all
ff = ForceField('my_charmm_ff.xml', 'qtip4pf.xml')
Do you think this is feasible? If not with CHARMM, would it be with Amber?
Thank you!
Joe
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Peter Eastman
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by Peter Eastman » Tue Feb 09, 2016 1:08 pm
If you're already starting from CHARMM files, what about just loading them directly with CharmmPsfFile?
Peter
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Joe Napoli
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- Joined: Fri Aug 09, 2013 12:09 pm
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by Joe Napoli » Tue Feb 09, 2016 1:25 pm
Hi Peter,
I am able to do that currently to run a gas phase simulation or a simulation in implicit solvent, but would I be able to load the charmm files directly, solvate the molecule, and run the simulation in explicit water (using e.g. TIP4P)?
Thank you!
Joe
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Jason Swails
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by Jason Swails » Tue Feb 09, 2016 1:29 pm
No, you would have to solvate the molecule with CHARMM or something equivalent. You could solvate in VMD and use autopsf to create the PSF file, or you could use CHARMM-GUI if you don't have access to CHARMM directly.
We're currently working on a CHARMM FF conversion, but it's not quite ready yet.