simtk.org • periodic boundary conditions for setup with Charmm files?

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periodic boundary conditions for setup with Charmm files?

Posted: Wed Jun 26, 2019 10:25 am

by fisiksnju

Hi,

I am trying to set up protein-ligand binding simulations with Charmm files (psf, str, prm) which already contains solvent and ions. But when I specify "nonbondedMethod=PME" in

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system = psf.createSystem(params, nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds)

, it generates error:

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Illegal nonbonded method for a non-periodic system

.

I checked the documentation, it seems that I could use

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system.setPeriodicBoxVectors()

to define the periodic box, but this requires the definition of "system" object which throws the error above.

Does anyone know how to solve this issue? Thanks!

Re: periodic boundary conditions for setup with Charmm files?

Posted: Wed Jun 26, 2019 10:31 am

by fisiksnju

Never mind, I found setBox() for psf file.

Thanks!