[gmx-users] scaling non-bonded interactions between groups

David van der Spoel spoel at xray.bmc.uu.se
Thu Nov 21 09:08:31 CET 2002

On Wed, 2002-11-20 at 16:10, Chris Page wrote:
> Hi,
> Rather than completely exclude all non-bonded interactions between two
> given groups, I would like to be able to scale them uniformly by an
> arbitrary factor.  Being relatively new to gromacs, I was wondering if
> anyone had any advice on what might be the simplest/safest way of
> implementing this (ie. that preferably doesn't involve hacking the inner
> loops)?
The only "simple way" to do this is to redefine the atomtypes of these
groups (i.e. create new atomtypes for the atoms in these groups) and
modify the nonbonded parameter matrix. This would not work for Coulomb

If you are prepared to hack the code you could use the energy group
exclusion mechanism to set a flag in the neighbourlist and pass other
parameters and an epsilon_r to the innerloops for just this group pair.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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