[gmx-users] Question about omega torsion
Bert de Groot
bgroot at gwdg.de
Wed May 12 15:36:11 CEST 2004
--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.
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
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