Re: bond lengths angles in namd

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Thu Jan 27 2011 - 07:14:26 CST

dear oguz gurbulak,

I see three options:

   - Use the extraBonds
feature<http://www.ks.uiuc.edu/Research/namd/2.7/ug/node26.html#SECTION00084400000000000000>
   .
   - Use NAMD's colvar module with a strong harmonic
restraint<http://www.ks.uiuc.edu/Research/namd/2.7/ug/node50.html#SECTION000123700000000000000>
   .
   - Modify the topology/parameter files and increase the bond/angle
   constant.

In all cases the length/angle will not be completly rigid, but the
fluctuations are inversely proportional to the restraining force.
Regards,
Ajasja

On Thu, Jan 27, 2011 at 12:43, oguz gurbulak <gurbulakoguz_at_yahoo.com> wrote:

> Dear All,
>
>
> I would like to ask if there is a possibility in NAMD to keep bond lengths
> or angles constant between two atoms and *among* three atoms ?
>
>
> Kind regards.
>
>

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