[gmx-users] freeze groups and com motion

[Berk Hess]

>From: David van der Spoel <spoel at xray.bmc.uu.se>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>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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