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

From: Markus K. Dahlgren (
Date: Tue Mar 13 2012 - 09:50:37 CDT

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.


Quoting Norman Geist <>:

> 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: [] 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.

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