[gmx-users] Re: freeze groups and com motion (Berk Hess)

[Zhou Bo]

Thanks to David and Berk. 
Another question is, if the movement of the monolayer in the z direction is
very small, drived by the Van de Waals interaction between the monolayer and
substrate, could I just stopcm the monolayer+water regardless of the
artifacts? Does the artifacts matter much in this case? I test two systems
with stopcm and without stopcm, the monolayer does move down to be adsorbed
on the substrate, but it drifts in xy plane in the system without stopcm.
The data after its adsoption is needed.
Thank you!

>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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