From: Charles Danko (dankoc_at_gmail.com)
Date: Mon Dec 20 2004 - 10:40:30 CST
Hi,
As far as I know, the restrain command will keep atom positions fixed
in space, not just fixed with relation to one another.
To set this up please conult the users guide page 54, as it gives an
ample tutorial.
Alternatively, you could fix the z-position of both atoms but allow
them to move through the xy plane.
Similarly, this information can be found on p53-54 of the NAMD manual.
The only think that confused me when I was learning was:
you have to make a new pdb file, and set the occupancy column to 1 for
the atoms which you wish to constrail.
Good luck!
Charles
On Mon, 20 Dec 2004 09:35:28 -0600 (CST), debashis.sikdar_at_ndsu.edu
<debashis.sikdar_at_ndsu.edu> wrote:
>
> Helo all,
>
> I want to run the molecular dynamics simulation keeping fixed distance in Z
> direction ( say 10 Angstorm ) between two sets of atoms.
>
> I found that there is a command 'restrain' in NAMD by which it can be done
> but how to use the restrin command in the configuration file i dont
> know....
> So any body can help how to use the restrain command in the configuration
> file to keep the fixed distance in Z direction between two sets of atoms?
> Thanks.
>
> Regards,
> Debashis
>
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