[gmx-users] center the system on specific atoms type

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Mar 15 11:33:03 CET 2012

Hey :)

Why would you want to keep it constant? It's asking for trouble. The
fluctuations in a small part of the system like a fullerene molecule
can be pretty large. If you try to correct the VCM of that bit only,
you make it constantly bump into your solvent molecules. Especially if
you have nstcomm = 10 or so, the shift may be considerable, and you
may cause overlaps and crash your system. And that while it's so easy
to center on the fullerene afterwards!



On Thu, Mar 15, 2012 at 11:16 AM, R.Perez Garcia
<r.perez.garcia at student.rug.nl> wrote:
>  Dear all,
> I am running a simulation in of a fullerene in different solvents. I would
> like to keep the fullerene somehow centred in the box, so I changed co
> comm_grps =  System to mm_grps  =  FUL.
> If I do this the following error pop up:
> There are:   395      Other residues
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
> NOTE 1 [file short1.mdp]:
>   4728 atoms are not part of any of the VCM groups
> WARNING 1 [file short1.mdp]:
>   Some atoms are not part of any center of mass motion removal group.
>   This may lead to artifacts.
>   In most cases one should use one group for the whole system.
> I am not sure if it is possible to tackle this....
> Any suggestion would be welcomed.
> Best regards: R
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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