From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Mar 14 2012 - 01:49:39 CDT
Unfortunately I don’t really understand your problem. If you align your
protein, vmd will move the whole system so that your protein is always on
the same place, thereas IMHO it cannot affect distances of your protein and
ligand. So what you see might be happening for real. Please explain what the
problem really is. And think of wrapping your system if the ligand is moving
far away, it’s maybe not, if is not done by namd already, but I think you
should wrap it before aligning it, this will cause a dancing box, but you
know you have the right unit center.
Good luck
Norman Geist.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Aron Broom
Gesendet: Dienstag, 13. März 2012 17:31
An: Markus K. Dahlgren
Cc: Namd Mailing List
Betreff: Re: AW: namd-l: center of mass movement removal throughout
simulation?
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.
~Aron
On Tue, Mar 13, 2012 at 10:50 AM, Markus K. Dahlgren
<markus.dahlgren_at_yale.edu> 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: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
Auftrag von Markus K. Dahlgren
Gesendet: Dienstag, 13. März 2012 00:54
An: namd-l_at_ks.uiuc.edu
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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