[gmx-users] Potential Energy

Yanmei Song ysong30 at asu.edu
Wed Jan 27 18:17:00 CET 2010

I did not develop the force field of my molecule by myself. In stead I use
the literature force field parameters. I guess not all the force field need
the [pairs]. As long as I can get reasonable experimental observables, I can
use such force field, right?

On Tue, Jan 26, 2010 at 6:50 PM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

> ----- Original Message -----
> From: Yanmei Song <ysong30 at asu.edu>
> Date: Wednesday, January 27, 2010 10:58
> Subject: Re: [gmx-users] Potential Energy
> To: jalemkul at vt.edu, Discussion list for GROMACS users <
> gmx-users at gromacs.org>
> > Dear Justin:
> >
> > I finally figure out that the problem comes from the Coulomb 1-4
> interactions defined by [pairs] part. When I remove this parts, the energy
> minimization ends with a big negative number. Thanks for your help.
> That's not a solution, that's a random number generator. Whether or not you
> need such pairs is force-field dependent. Ad hoc changes are ridiculous.
> Messing with force fields is an expert topic, and parameterizing a new
> molecule is difficult and risky.
> Mark
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Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
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