Re: Constrain=?ISO-8859-1?Q? centers of mass for ?= selected atoms

From: michael_at_perfect-kreim.de
Date: Thu Feb 07 2008 - 07:03:17 CST

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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