[gmx-users] misunderstanding comm-grps

[Dallas Warren]

What do you mean by "stay in the center of the box"?

Since systems are run using the periodic boundary condition (PBC), what you
essentially have is an infinite, repeating box in all directions.  And what
is the center of that box is entirely arbitrary, you can place it wherever
you like.  And you can apply that after the completiion of the simulation.

See http://manual.gromacs.org/current/user-guide/terminology.html#gmx-pbc

The removal of center of mass motion is applied in MDS to avoid the flying
ice cube phenomena.  That happens when all the molecules lock together into
a crystal like structure, hardly moving relative to each other, freezing in
place, but the entire group of molecules are moving together (hence the
center of mass) at high speed.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Tue, 4 Feb 2020 at 11:34, Miro Astore <miro.astore at gmail.com> 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
>                                   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?
>
> Best, Miro
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