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

[Berk Hess]

>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.