[gmx-users] Question about omega torsion

[Bert de Groot]

--Hua Wong wrote:
> After some time fiddling with the parameters of the new minimisation engines (both CG or SD), I think I got them pretty much in hand now. It works pretty well.
> 
> However, I still find omega angle torsion deviation (using procheck), although lesser than with NAMD for example. Is there any other parameters I can refine in order to decrease (or make vanish) the number of peptide omega angles deviation?
> 


this is a known "feature" of most MD protein force fields. What you can do is to
increase the force constant for the omega torsion angle. For minimisation you can do so
without problems, but I wouldn't recommend it for MD, since it might affect the dynamics
in undesired ways.

--

Bert

____________________________________________________________________________
Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany

tel: +49-551-2012308, fax: +49-551-2012302

email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/073
____________________________________________________________________________