[gmx-users] evaporating system
acosta at vdov.net
Tue Oct 21 02:50:44 CEST 2008
> I don't understand how you manage to simulate in the NVT ensemble
> without using pbc or any other way to define the limits of your
> system? How do you then make a difference with NVE?
Hmm ... pretty simple perhaps I'm doing something wrong. I generate a
frozen box of the water and my solute and gradually warm it up in the
NVT ensemble. I'm looking to study the droplet evaporation in full
vacuum. I am also using an angular comm_mode for both the solvent and
the solute in this system, which I forgot to mention previously.
Otherwise my simulation setup is entirely unremarkable.
> To avoid molecules to go far far far away you can define a dummy
> atom at the center of your system and define distance restraint.
> The water molecules would not be able to further than a given
> distance. You might have to define a lot of distance restraints, though!
I will look at the manual on this. Seems it would be fairly simple to
write a little something to generate these constraints automatically
for all the water in my system.
Perhaps I have gone about this all wrong for my spherical droplet
evaporation in vacuum. If you have any recommendation, that would be
Anthony B. Costa
Department of Chemistry
560 Oval Drive, #365
West Lafayette, IN 47907
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