[gmx-users] density and intramolecular interactions

Mark Abraham Mark.Abraham at anu.edu.au
Fri Sep 11 15:56:45 CEST 2009

Alexey Odinokov wrote:
> Hi everyone,
> I have a model for liquid benzene. In this model all bonds are treated as
> harmonic potentials. When I use larger constants for these potentials (to
> make molecules more planar), the average density of my benzene (from NPT
> ensemble) becomes lower. Does virial depend on intramolecular interactions?

See manual Appendix B.

> If a want to make benzene molecules completely rigid (through the virtual
> sites, for example), can I use the same parameters for intermolecular
> interactions?

That depends on how the parameters were developed. In general, assume 
nothing until you've demonstrated they might be transferable to a new 


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