[gmx-users] Specifics on tabulated pair potentials

MURAT OZTURK murozturk at ku.edu.tr
Thu Sep 20 12:10:43 CEST 2012


I am using gromacs for coarse grained systems. I have the need to represent
breakable bonds. I have been using tabulated lennard-jones-cosine
potentials with bonded interactions but now there is a need for proper
non-bonded interactions on specific pairs.

I have went through the manual but there seems to be very limited
information on 'pair' interactions.

Normally, I set my functypes to 8 or 9 for bonds, angles and dihedrals, and
name the tables accordingly (table_b1.xvg etc.) I also have tabulated
non-bonded interactions which I set up in the .mdp file. I have their
tables with the appropriate names such as (table_S_P.xvg etc.). When I run
mdrun with no special parameters, everything works nicely with all these

I understand how I can add pair interactions in the topology file, but the
function types are limited to 1 or 2, which I don't want to use. I want to
use a tabulated potential. I understand that there is an option -tablep in
mdrun, but I can't seem to understand how the whole thing works.

So I want to have tabulated non-bonded interactions between specific pairs
of (super)atoms. Is this possible and how should I go about doing that?

Thanks in advance. I have been working on this project for a year,
occasionally lurking on the mail list archives. This is the first mail I am
sending. I truly appreciate the effort that is put into making and
supporting this code. Cheers to you all.


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