[gmx-users] osmotic pressure in Gromacs

[David van der Spoel]

杭军 陆 wrote:
> Hi,
> 
> */   We want to simulate water transport through channel by osmotic 
> pressurce using Gromacs software. The force on the water molecules is 
> usually applied only in a buffer zone, not on all water molecules. How 
> to set up my system. In my opion, we can only define a simple group by 
> index. Water molecules are moving, so the water molecules in a buffer 
> zone change frequently. How to define the group of water molecules in a 
> buffer zone. Gromacs can do it?/*
> */  thanks!/*

Of course. How do you model the channel?
If you put two membranes like this:

Water

=== membrane ====

Water with salt

=== membrane ====

Water (periodic)

the membrane will probably break sponteously. Look for papers by Ilpo
Vattulainen on this topic.


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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se