[gmx-users] User Defined Potentials

hassanal at purdue.edu hassanal at purdue.edu
Mon Sep 12 22:51:23 CEST 2005

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?

Thanks for your help in advance.

Ali Hassanali

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