[gmx-users] flying water on monolayer

McMullen, Roger L RMcMullen at ispcorp.com
Fri Nov 12 18:32:31 CET 2004

Bon Dia Hector.  The reference below is a good source for this problem.
They constructed a dual monolayer system separated by a slab of water.  In
this manner, they were able to keep the water in place and also to apply
periodic boundary conditions only in x and y.

Ahlstrom, P. and H. J. C. Berendsen (1993). "A molecular dynamics study of
lecithin monolayers." Journal of Physical Chemistry 97(51): 13691-702.

In addition, we did some work in this area using several different force
fields.  We found that the Gromos 96 forcefield which is modified for lipid
tails (I think it is ffG43a2.), provides the best results.


-----Original Message-----
From: Hector Martinez-Seara Monne [mailto:h.seara at qf.ub.es]
Sent: Friday, November 12, 2004 10:26 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] flying water on monolayer

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

   Hector Martínez-Seara Monné

            Universidad de Barcelona
                Dept. Química Fisica

         hseara at netscape.net
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