Re: AW: center of mass movement removal throughout simulation?

From: Aron Broom (
Date: Tue Mar 13 2012 - 11:30:38 CDT

I don't think center of mass motion is your problem here. Even if it was
removed every frame, you would still get the behaviour you observe, because
it is the center of your ENTIRE system that is being fixed, which includes
the solvent. So it is totally reasonable to expect your protein and ligand
to drift around inside the box.

Once you've aligned your protein backbone, you need to recenter the
periodic box around your protein. I'm not sure of the exact command for
this, but I believe this is a trivial problem that does not require any
special new implementations.


On Tue, Mar 13, 2012 at 10:50 AM, Markus K. Dahlgren <> wrote:

> This works if it was not for my ligands. Usually the protein can be
> aligned, but
> then the ligand would leave the protein for X number of frames and come
> back and
> then leave again. I have not been able to resolve this with the PBC tools
> or the
> RMSD trajectory tools.
> Best,
> Markus
> Quoting Norman Geist <norman.geist_at_uni-greifswald.**de<>
> >:
> Also Markus to view your protein you can also just use the RMDS Trajectory
>> Tool in VMD to align your protein over the frames by its backbone and an
>> reference frame so it will no more move away (basically just press align).
>> cheers
>> Norman Geist.
>> -----Ursprüngliche Nachricht-----
>>> Von: [mailto:owner-namd-l_at_ks.uiuc.**edu<>]
>>> Im
>>> Auftrag von Markus K. Dahlgren
>>> Gesendet: Dienstag, 13. März 2012 00:54
>>> An:
>>> Betreff: namd-l: center of mass movement removal throughout simulation?
>>> Hi!
>>> I have seen that there have been mailing list mails asking this before,
>>> but I
>>> did not find a post where it was resolved.
>>> The COMmotion keyword in NAMD removes the center of mass movement. But
>>> it only
>>> does it initially. After a while my protein complexes start to move
>>> around in
>>> the box and it becomes a mess trying to view the trajectory after using
>>> the PBC
>>> plugin.
>>> Is there a way in NAMD to remove the center of mass movement every
>>> frame? This
>>> if possible in some other MD software, such as OpenMM. If it is not
>>> possible to
>>> do this every frame, can I put in a feature request for future
>>> developments for
>>> this?
>>> Any insight would be greatly appreciated.

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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