[gmx-users] Soft-core Coulomb potential

Samuel Genheden samuel.genheden at gmail.com
Thu Feb 21 15:55:41 CET 2013

Hi, everyone

I'm new to using Gromacs, so pardon me if this question has been up
for discussion before.

I want to calculate free energies of decoupling solutes from a bath of
solvent molecules. And I want to decouple the charges and the van der
Waals parameters simultaneously. This is fantastically easy to setup
in Gromacs, but I'm curious about the implementation of the soft-core
Coulomb potential.

I do not think it is clear from the manual the exact functional form
of the soft-core Coulomb potential. The manual can be read as it uses
the same modified distance as the Lennard-Jones potential, which
includes a sigma-dependece, something that seems strange to me. Is
this the case?

Secondly, it is common to assign different values to the alpha
parameter for the Coulomb and Lennard-Jones parameters. However, this
seem not be the case, since there is only one sc-alpha input
parameter. Am I correct in this assumption as well?

I would also like to have some pointers where, in the code, the
soft-core is implemented so that I could modify it if I find it

Best regards,
Samuel Genheden
Postdoctoral Research Fellow
School of Chemistry
University of Southampton
Highfield, Southampton
SO17 1BJ

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