[gmx-users] misunderstanding comm-grps

[Justin Lemkul]

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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