Re: Constrain centers of mass for selected atoms

From: poker_at_physics.usyd.edu.au
Date: Thu Feb 07 2008 - 18:36:00 CST

What you want instead is an customised TclForces script.

Read this section of the NAMD userguide:
http://www.ks.uiuc.edu/Research/namd/2.6/ug/node33.html#SECTION00096800000000000000

the addgroup command will get you the COM coordinate.

The example script in there should get you started; come back if you have a
specific trouble and post the non-working script you've written so far.

P.

Quoting michael_at_perfect-kreim.de:

> Hello,
>
> I found this Mail in the NAMD-List-Archive:
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/5187.html
>
> They say there, that it is possible to use a Steered-MD with velocity=0.
> But I do not understand what I have to set as direction-vector SMDDir,
> to hold the atomselect in place.
> I thought that I need (0 0 0) as vector, but in this mail the vector is
> (1 1 1).
>
> Can you please explain this to me?
>
> Thanks a lot,
>
> Michael
>
> > Hello,
> >
> > is it possible to constrain the center of mass of an atom-selection in
> > NAMD?
> > I am looking for a way to hold my protein in the middle of my
> > simulation-box during simulation.
> >
> > For charmm there exists a command
> > CONS HMCM FORCe real [WEIGhting] reference-spec atom-selection
> >
>
http://www.charmm.org/old_site/document/Charmm/c30b1/cons.html#%20Center%20of%20Mass
> >
> > In principle this is what I need.
> >
> > Can you please give me any hinds how to do this in NAMD?
> >
> > Thanks a lot and best regards,
> >
> > Michael
>
>
>
>

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