From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Mon Sep 04 2006 - 16:17:31 CDT
The free energy restraints are only active inside a pmf or mcti block; see
"Options for Potential of Mean Force Calculation" in the manual. You can
do similar types of things with TclForces, but it's not as automated.
-Jim
On Sun, 3 Sep 2006, Neelanjana Sengupta wrote:
> Hi,
> 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
> calculations:
> 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??
>
> Thanks,
> Neela
>
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