AW: center of mass movement removal throughout simulation?

From: Norman Geist (
Date: Tue Mar 13 2012 - 01:36:16 CDT

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).


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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