From: David van der Spoel <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: Discussion list for GROMACS users <[email protected]>
Subject: Re: [gmx-users] freeze groups and com motion
Date: Thu, 06 Sep 2007 19:34:31 +0200
Zhou Bo wrote:
Dear Fellow Users,
I am modeling a system of a monolayer adsorbed on a water/solid
interface. I just freeze the solid substrate, and I use ewald_geometry =
3dc in the mdp file (a vaccum boundary is upon the water). As the mass of
the monolayer is 3 times less than the substrate, and 13 times less than
the solvent, I am not sure whether or not I should remove the com motion
of the whole system. Does anyone have any suggestions?
don't do anything else to stuff you've frozen (e.g. no constraints either).
you can stopcm the monolayer+water, or separate.
What you would want is stopcm only the xy components of monolayer+water.
If you also stop z you get artifacts, as you have an absolute reference in
z.
I think that in the current version this is not possible.
In Gromacs 4.0 this will be possible with uniform walls.
But we probably should add a xy only mdp option for stopcom.
Berk.
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