RE: deformations in a water box during equilibration in NAMD

From: JC Gumbart (
Date: Fri Nov 03 2006 - 09:57:39 CST

If you simulate a pure water box made from Solvate, I don't expect it would
deform under constant pressure. However, with a protein, there are still
many empty spaces after solvating, possibly inside the protein and
definitely around it. Hence, water has to fill those spaces during
equilibration, and if you're starting with CV, you won't have enough water
in total to fill the volume.

-----Original Message-----
From: [] On Behalf
Of Alessandro Cembran
Sent: Friday, November 03, 2006 9:43 AM
Subject: Re: namd-l: deformations in a water box during equilibration in

You can find the solvate package in
~/lib/vmd/plugins/noarch/tcl/solvate1.2/ (or wherever you decided the
vmd libs have to be installed in your config file).
My guess is that they are using a pre-equilibrated w-box in wat.pdb.
Anyway, the fact that the box gets deformed during equilibration cannot
be related to the equilibration state of the water molecules. I would
say that the problem might be related to the PBC definitions. What unit
cell shape are you using? Cubic? What are your three vectors? Are you
doing NVT or NPT? What kind of deformation does the box undergo?

Alessandro wrote:
> Hello!
> Anybody knows how works the solvate module in VMD (used for NAMD)?
> When I do
> pakage require solvate
> solvate protein.psf protein.pdb -t 5 -o outputname
> is the programm creating boxes of water molecules miminized and
> equilibrated or only molecules of water dispersed?
> If I use the solvated protein created from this module for a
> minimization and subsequent equilibration in NAMD, the water box is
> deformed during equilibration. If the boxes of water are not
> equilibrated, I suppose this could be the reason??
> Thanks a lot in advanced.
> Best wishes,
> Rebeca García
> Post-doctoral researcher
> Universidad de Barcelona

Alessandro Cembran,PhD
Post Doctoral Associate
Mailing Address:
Univ. of Minnesota, Dept. of Chemistry
G2, 139 Smith Hall 207 Pleasant St SE
Minneapolis, MN 55455-0431
Univ. of Minnesota, Walter Library
117 Pleasant St SE, Room 473
Phone: +1 612-624-4617

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