[gmx-users] NEW SOLVENT - DMF box equilibration

[Christoph Freudenberger]

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.
-- 
Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785