Re: Fixed COM

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Mon Jul 11 2011 - 14:37:43 CDT

Hi,

If you would like to restrain just the COM of the molecule (and allow for
rotations and structural changes within the macromolecule) a better option
is to define the COM as a colvar and use harmonic restraints on the COM
colvar.

the colvars module: http://www.ks.uiuc.edu/Research/namd/2.8/ug/node53.html
harmonic restraints on the colvar:
http://www.ks.uiuc.edu/Research/namd/2.8/ug/node56.html#SECTION000133700000000000000

Regards,
Ajasja

On Mon, Jul 11, 2011 at 20:52, Parisa Akhski
<Parisa.Akhshi_at_chem.queensu.ca>wrote:

> **
>
> Hi,
>
> Below, please find the instruction to fix the atoms if you know the atom
> numbers of the COM of your molecule:
>
> http://www.ks.uiuc.edu/Research/namd/2.6/ug/node28.html
>
> Parisa
>
>
>
> -----Original Message-----
> From: owner-namd-l_at_ks.uiuc.edu on behalf of Ali Khanlarkhani
> Sent: Mon 7/11/2011 2:30 PM
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: Fixed COM
>
> Dear all,
>
> I want keep center of mass of the molecule fixed in the MD simulation, can
> I do
> this?
>
> Thank you,
> Regards,
> Ali Khanlarkhani
>
>

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