Re: 1-5 Intramolecular repulsions

From: Kenno Vanommeslaeghe (
Date: Wed Nov 05 2014 - 12:33:12 CST

While the answer is in all likelihood "no", the question is poorly
formulated; I read it a few times over and I'm still confused about what
exactly you're looking for (and I work on force fields on a daily basis).
Do you mean "exceptions" instead of "interactions"? Also, if you want an
R^-12 repulsion without R^-6 attraction (which raises questions about the
rationale behind the force field), you also have to worry about whether
NAMD lets you specify them separately (I honestly don't know). Finally,
your "for example" link doesn't work; it likely relies on form data that
is not contained in the URL.

On 11/05/2014 12:54 PM, Rebecca Lindsey wrote:
> Dear All,
> Is there a way to include 1-5 (intramolecular) interactions in NAMD? As
> far as I understand, neither NBFIX nor NBTABLE can be used to accomplish
> this, as do not allow for a distinction between intra- and inter-molecular
> interactions.
> The repulsion term in question would be along the lines of: E_repel =
> a_repel/(r_ij)^12, as it is given by the TraPPE force field. (see, for
> example:
> Thanks in advance for your insights.
> --
> Rebecca K. Lindsey
> ----------------------------------------------------
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