problem with Dihedral Restraints

From: Neelanjana Sengupta (
Date: Mon Sep 04 2006 - 01:13:44 CDT

I am simulating a small peptide, and need to constrain its torsional angles
to desired values. I am doing this via NAMD's freeEnergy Conformational
freeEnergy on
freeEnergyConfig DiheRestrs.inp

where in my restraint file DiheRestrs.inp, I provide the foll. (including
every dihedral, of course):

urestraint {
dihe (VAL8, 3, CA) (VAL8, 3, C) (VAL8, 4, N) (VAL8, 4, CA) barr=500 ref=-60
dihe bound (VAL8, 3, CA) (VAL8, 3, C) (VAL8, 4, N) (VAL8, 4, CA) gap=450
low=-150 hi=-90 delta=10

dihe (VAL8, 3, C) (VAL8, 4, N) (VAL8, 4, CA) (VAL8, 4, C) barr=500 ref=-60
dihe bound (VAL8, 3, C) (VAL8, 4, N) (VAL8, 4, CA) (VAL8, 4, C) gap=450
low=-70 hi=-55 delta=10

Inspite of using such a high force constant, I DO NOT observe any change in
the dihedral distribution, even after a 1 ns simulation. Could somebody
point out if I am doing something wrong, or, if I need to run very, very
long to reach the desired configuration??


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