[gmx-users] Ramachandran Plot

[Mungikar, Amol Arvind (UMR-Student)]

dear gmx-users,

This may sound very trivial! But, here it goes ...After solvating a
small 8-residue peptide (there is no glycine in my peptide) in water for
10 ns, the peptide structure I am getting at the end of 10ns shows
torsion angles phi and psi angles going in the disallowed regions of
Ramachandran Plot. Well, I know that this is not the 'representative'
structure of the peptide! But, is there any way to avoid going in the
disallowed regions of the Ramachandran Plot, or maybe I am doing
something wrong!! 
Is there any way I can constraint only the omega (C-N) angle while
keeping phi and psi free?
I request all of you to kindly help me understand the concept. Thank you
very much in advance.

Amol A Mungikar
Graduate Student
University of Missouri, Rolla
MO USA 65401
Email: Mungikar at umr.edu