Re: Intermolecular potential energy function in NAMD

From: Kenno Vanommeslaeghe (
Date: Fri Aug 01 2014 - 11:41:46 CDT

You might be confused about the meaning of the term "intermolecular
potential energy function" in whatever context you found it in. You might
want to show the source to your supervisor and discuss it with her or him.

As far as I can see, all you need to do is tell NAMD to use the
appropriate nonbonded settings for OPLS (including combining rules,
cutoffs and switching functions).

If the chloroform model is completely rigid (even the chlorines), you also
need to somehow convince NAMD of that. I don't know how to accomplish
this, but the experts on this list probably do.

On 08/01/2014 07:31 AM, Viswanath Pasumarthi wrote:
> Hi,
> I'm trying to simulate the demixing process of bulk water+chloroform using
> NAMD. The respective TIP3P and OPLS models use intermolecular potential
> energy functions. How is it possible to define rigid monomers of water and
> chloroform followed by implementation of the intermolecular potential
> energy function in NAMD? I have knowledge of performing simulations using
> atom-based potential energy function which uses atom-based cutoff.
> Thanks in advance.

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