[gmx-users] evaporating system

Xavier Periole X.Periole at rug.nl
Tue Oct 21 15:00:03 CEST 2008

On Mon, 20 Oct 2008 20:50:44 -0400
  "Anthony Costa" <acosta at vdov.net> wrote:
>> 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.
How do you keep your volume constant? Or is it constantly infinite?
That might well be!
The difference with NVE is something else, sorry!
>> 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
> --
> Anthony B. Costa
> Purdue University
> Department of Chemistry
> 560 Oval Drive, #365
> West Lafayette, IN 47907
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XAvier Periole - PhD

- Molecular Dynamics Group -
NMR and Computation
University of Groningen
The Netherlands

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