[gmx-users] misunderstanding comm-grps

[Miro Astore]

Oh thank you very much I think I got confused looking at older documentation.

What sort of artefacts get created by using

comm-grps = Protein non-Protein?

On Wed, Feb 5, 2020 at 11:14 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> On 2/3/20 7:33 PM, Miro Astore wrote:
> > Hi everyone,
> >
> > I have tried using comm_grps to try and remove center of mass motion
> > from my system.
> >
> > I used the following configuration
> >
> > comm_grps               = non-Protein Protein
> > nstcomm                 = 100
> > comm_mode               = linear
> > comm_grps               = non-Protein Protein
>
> Don't do this. Multiple COM motion removal groups are only appropriate
> in layered systems that have different diffusion behavior.
>
>
> >                                    refcoord_scaling        = com
> >
> > But I still get considerable drift in my protein. Am I
> > misunderstanding what comm is actually doing and I should use the
> > pulling code if I want my protein to stay in the center of the box?
>
> Dallas covered this nicely. The algorithm does not (and is not intended
> to) prevent diffusion. It subtracts erroneous contributions to the
> kinetic energy in the system.
>
> -Justin
>
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
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