Running a small molecule using CHARMM ff and explicit H2O

[Joe Napoli]

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

[Peter Eastman]

If you're already starting from CHARMM files, what about just loading them directly with CharmmPsfFile?

Peter

[Joe Napoli]

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

[Jason Swails]

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.