[gmx-users] NEW SOLVENT - DMF box equilibration

jiri vondrasek jirka at uochb.cas.cz
Fri Jul 11 10:53:00 CEST 2003

Well, the equilibration is done (running for 2ns at 300k/1bar) but the
density is a little bit higher than published. I have been wondering if
I can controll it (better say decrease it) by let say vdw parameter.
thank you


On Fri, 2003-07-11 at 04:30, Christoph Freudenberger wrote:
> jiri vondrasek wrote:
> > Hello
> > I have created a box of DMF (N,N-dimethylformamide)after a long "try and
> > error" period. Now I am a little bit uncertain if I set up everything
> > well. Would anybody tell me how to specify density or what kind of
> > parameters can help me in setting up a density close to the experimental
> > value? Does anybody have a mdp file for equilibration of solvent box?
> > Getting such file with explanation will be greatly appreciated. thanks
> > jiri
> You should just perform equilibration by MD at 300K/1bar. The box vectors will
> be scaled to (hopefully) reproduce the correct density.
> You should also check DHvap and the diffusion coefficient against
> literature values (both MD and exp.!).
> See Davids response for examples of run-input files.
jiri vondrasek <jirka at uochb.cas.cz>

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