Re: restraining the COM of a group of atoms

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Sat Oct 10 2009 - 15:03:52 CDT

Hi Bin,

Yes, the colvars module can be used for that in NAMD 2.7b1. The
reference position could be specified using a dummy atom group, see
the dummyAtom keyword here:
http://www.ks.uiuc.edu/Research/namd/2.7b1/ug/node48.html#SECTION000122300000000000000

As a side note, though: the fact that lots of people want to do it
doesn't mean it's a good idea - in most cases anyway.

Cheers,
Jerome

2009/10/10 BIN ZHANG <zhngbn_at_gmail.com>:
> 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
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:51:33 CST