From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Nov 24 2010 - 13:05:31 CST
On Wed, Nov 24, 2010 at 12:29 PM, Thomas C. Bishop <bishop_at_tulane.edu> wrote:
> Anyone ever implement morse potentials in NAMD.?
> there was a question about this earlier. see
>
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/4621.html
>
> Thanks in advance for any info.
>
> Aside from the coding part how should one represent this in the topology file (psf) ?
the psf file does not provide _any_ information about
the force field parameters. only the atom types.
those atom types are then matched against the parameter file
and then the parameters for each pair of atom types generated
through mixing rules. those can then be overridden by NBFIX
entries, if needed.
you probably need to write a modified parser for this,
or just define a new parameter file format.
the question is, for what you want to use this.
perhaps it might be simpler to use an MD
code that already supports morse potentials (there are
several), or use tabulated potentials.
cheers,
axel.
>
> Tom
>
> *******************************
> Thomas C. Bishop
> Tel: 504-862-3370
> Fax: 504-862-8392
> http://dna.ccs.tulane.edu
> ********************************
>
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
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