[gmx-users] evaporating system

Anthony Costa 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
much appreciated.

Thanks again,

Anthony B. Costa
Purdue University
Department of Chemistry
560 Oval Drive, #365
West Lafayette, IN 47907

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