[gmx-users] extra potential term in gromacs

Felicia Pitici fp42 at cornell.edu
Mon Jul 13 17:59:20 CEST 2009


I would appreciate if someone could help with advice regarding including
the effects of an extra LJ repulsive term in Gromacs. Would this be
possible to do this without actually altering the functional form?

The extra repulsive term is applied to one single type of atom pairs. I
thought of adding this 1-5 atom pair as a fake 1-4 pair to the 1-4 list,
with the appropriate change in the LJ 12-constant. However, since the
intramolecular 1-4 electrostatics is scaled by 1/2, the respective Coulomb
term for this fake 1-4 pair will be only half the actual value. And then,
I do not know how to account for the missed 1/2 electrostatics.

Is there anything else I could do before considering altering the
potential function? Thank you for helping me out.



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