[gmx-users] Symmetry

Bert de Groot bgroot at gwdg.de
Tue Oct 1 09:22:07 CEST 2002

David wrote:
> On Mon, 2002-09-30 at 20:19, Shrivastava, Indira (NIH/NCI) wrote:
> >
> >  Hi gromacs users,
> >
> >  Is it possible to apply symmetry restraints to a protein during MD run?
> >  eg if my protein has a four-fold symmetry, would it be possible to apply
> >  a restrain which will maintain this symmetry during MD?
> >  More importantly, would it be 'correct' to do such a simulation or is it
> >  too biased??
> It is not possible right now, although it would be good to have
> something like this. It should then be possible to simulate crystals
> using the assymetric unit rather than the whole unit cell.

I have written a crystallographic refinement module (both reciprocal and
real space, to be used with gmx 2.0) that handles symmetry, either as 
contraints or restraints. This code isn't completele ready for production 
(which is why it was never committed), but if somebody is interested, 
please let me know.


Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de

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