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

[hassanal at purdue.edu]

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?

Ali