restraining the COM of a group of atoms

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Fri Oct 09 2009 - 19:19:56 CDT

Hi, All:

Browsing through the mailing list, I saw quite a few people interested
in restraining the center of mass (COM) of a group of atoms during
their simulation. However, to my understanding, NAMD does not have an
elegant way to do this (correct?). Though tclforces script could do
the job, it would be a pain while the number of atoms is big.

So my question is why does NAMD not offering this ability? It cannot
be a coding issue. Actually, I think it's rather trivial to implement
this, given that it already has SMD implemented. It should be
basically the same as SMD, except here we have zero velocity, and also
the moving direction is updated on the fly as r - r0.

Am I missing something here? Is NAMD 2.7b1 already able to do this? If
not, I would like to try to do it myself.

Thanks for any comments.

Best,
Bin

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