[gmx-users] User Defined Potentials

David van der Spoel spoel at xray.bmc.uu.se
Tue Sep 13 08:31:20 CEST 2005

On Mon, 2005-09-12 at 15:51 -0500, hassanal at purdue.edu wrote:
> Gromacs Users,
> I would like to insert an "additional" potential of the form 10-12 between 2
> specific atoms in my system to model the underestimated pi-cation interaction
> purely given by a LJ 6-12 interaction. I understand that user defined potentials
> are put in table format but I can't see any description on how to specify the
> atom  pair that it will be applied to. It looks as though the user defined
> potential will automatically be applied to all LJ pairs in the topology file. Is
> this a correct observation or not? 
> Would it be possible to add a potential of the form 10-12 (without going into
> the guts of gromacs code) and to add it to only 1 pair of atoms in my system?
How about using a Morse bond instead?

What you ask is not trivial...

> Thanks for your help in advance.
> Ali Hassanali
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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