problem with dihedral restraint

From: Neelanjana Sengupta (
Date: Fri Oct 06 2006 - 16:11:43 CDT


I am trying to do a restraint simulation, where a small peptide, initially
in the 3-10 helical configuration, is forced to be in the alpha-helix
configuration. I believe this can be done through the free Energy
Calculations method on NAMD. I include these commands in my NAMD input file:

freeEnergy on
freeEnergyConfig DiheRestrs.inp

where my DiheRestrs.inp file includes restraint values for each (phi, psi),
the upper and lower limts, and the force constants:

urestraint {
dihe (VAL8, 2, CA) (VAL8, 2, C) (VAL8, 3, N) (VAL8, 3, CA) barr=500 ref=-70
dihe bound (VAL8, 2, CA) (VAL8, 2, C) (VAL8, 3, N) (VAL8, 3, CA) gap=20
low=-120 hi=-67 delta=10
dihe (VAL8, 2, C) (VAL8, 3, N) (VAL8, 3, CA) (VAL8, 3, C) barr=300 ref=-50
dihe bound (VAL8, 2, C) (VAL8, 3, N) (VAL8, 3, CA) (VAL8, 3, C) gap=20
low=-67 hi=-47 delta=10

As you see, I am using a very high barrier. However, my system is just NOT
doing what it should do.... In fact, the (phi, psi) do not change at all
from the original values!!

Your suggestions/corrections are highly appreciated.
Thanks and regards,

Neelanjana Sengupta
Graduate Student
Dept of Chemistry
Univ. of California, Irvine
Irvine, CA 92617
Phone: 949 824 9921

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