[gmx-users] flying water on monolayer
jake at ncsa.uiuc.edu
Sun Nov 14 23:49:37 CET 2004
Water does indeed have a non-zero vapor pressure--even simulated water.
At 11:10 AM 11/12/2004, you wrote:
> > Hi all (sorry for send it again),
> > I'm simulating a monolayer in gromacs 3.2.1. I have a brief question
> > that maybe someone more experimented has just due with. The fact is that
> > everything seems to be all right except that some waters (6 of 20000)
> > fly away from the bottom of the layer of water under the monolayer till
> > reach the the top of the monolayer ( I'm using periodic conditions xyz),
> > some of them remain there some time then they come back to the water
> > layer but in fact there's always an average of water molecules in the
> > top of my monolayer. The force field that I'm using is GROMACS (
> > gromos-87 + extended) and the water are SPC. That's normal? there's any
> > way to fix it? There are any significant change for that I have to take
> > in consideration?
> > Thank you, Hector
>There are two ways to solve this:
>1) To impose a potential that keeps the waters in the bulk.
>2) To replicate another monolayer in the "top" and to enlarge the Z
>so the lipid tails will only see vacuum:
>In this case, even with periodic boundary conditions in Z, tails from the two
>monolayers will not see each other.
>Pedro Alexandre Lapido Loureiro
>Laboratório de Física Biológica
>Instituto de Biofísica
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Eric Jakobsson, Ph.D.
Professor, Molecular and Integrative Physiology, Biophysics and
Computational Biology, Beckman Institute, Bioengineering, Biochemistry, and
Senior Research Scientist, National Center for Supercomputing Applications
4021 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews Avenue
Urbana, IL 61801
e-mail jake at ncsa.uiuc.edu
(Since May 2003 I have been on leave from the University of Illinois to
serve as the Chair of the NIH Biomedical Information Science and Technology
Consortium and the NIGMS Center for Bioinformatics and Computational
Biology, in Bethesda, Maryland. However I commute to Urbana almost every
week to maintain my research lab here.
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