[gmx-users] Having WCA bonded interaction with FENE potential

ARNAB MUKHERJEE arnabmukherjee249 at gmail.com
Tue Jan 24 15:40:24 CET 2017


I am simulating a charged bead-spring modelled polyelectrolyte with FENE
bond stretching potential and Deby Huckel potential for electrostatics. I
need to combine FENE bonded interaction combined with WCA potential,
otherwise the beads overlap with each other since there is no replusive
term. Before this I ran the same system with no electrostatics, so to take
into account WCA for bonded interaction I did No. of bonded exclusions
nexcl = 0, and the results of the simulation seem to be ok.

Now for the same system with electrostatics, if I do nexcl = 0, then there
will also be electrostatic repulsion between the bonded beads, which I do
not want. So, how can I have WCA interaction between the bonded atoms,
without having electrostatic interaction between them?

I know in worst case, I can build a table for the bond stretching
potential, where I can add the WCA term with FENE potential. But is there
an easier way to do this? As FENE potential is already there as one of the
bonded interactions in gromacs.

Thanks a lot,


Arnab Mukherjee

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