[gmx-users] gromacs-3.3 and User defined Potentials

hassanal at purdue.edu hassanal at purdue.edu
Tue Sep 13 17:34:10 CEST 2005

Thanks Berk, that certainly helped. One last question though. In the regular
tables, the parameter values and charges are read from the topology file. With
the energygrouptables  where and how does it read the input parameters. For
example, in the documentation it mentions an Na Na pair wise interaction which
should be put in table_Na_Na.xvg; if I am modeling Na--Na with a A/r^10 - B/r^12
 (for the sake of argument) do those just go into the table file itself without
having to add anything to the .itp or topology files?


Quoting Berk Hess <gmx3 at hotmail.com>:

> >From: hassanal at purdue.edu
> >Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >To: gmx-users at gromacs.org
> >Subject: [gmx-users] gromacs-3.3 and User defined Potentials
> >Date: Tue, 13 Sep 2005 10:08:21 -0500
> >
> >Gromacs Users,
> >
> >I compiled the beta version of gromacs with the hope of trying the option 
> >that
> >3.3 version has of defining different potentials between atom types. 
> >However I
> >need some help on how to get this going because of no documentation 
> >available
> >yet. I noticed that the "mdrun" option has a - tablep.xvg option with it 
> >which
> >is for pair-wise atom potentials. Does my "user defined potential" go into 
> >there
> >as before? How and where do I specify which atoms to apply it to? Someone 
> >had
> >mentioned earlier on that this could be done by defining separate energy 
> >groups
> >for that pair of atoms. If I do defined my atoms in a seperate energy group
> >in
> >the mdp file, is there a way (in gromacs 3.3) to ask it to apply my
> >"user-defined-potential" to that energy group using the tablep.xvg file?
> This feature is documented in:
> share/html/online/mdp_opt.html
> Berk.
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