urestraint for minimizations and MD (no PMF)

From: MW Van der Kamp, School of Chemistry (Marc.VanderKamp_at_bristol.ac.uk)
Date: Thu Nov 02 2006 - 05:46:21 CST


I've been trying to apply some distance restraints for specific atoms in my
system. I would like to use the 'urestraint' command, as I prefer only to
apply a restraint force when the distance exceeds a certain value (single
sided harmonic).

This is what I initially tried:

 freeEnergy on
 freeEnergyConfig {
 urestraint {
 dist bound (MAPP, 1, O1) (PROA, 233, CE1) kf=50 hi=3
 dist bound (MAPP, 1, O2) (PROA, 233, CE2) kf=50 hi=3

It seems to be read in ok in the output:
 Info: ***********************************

 urestraint {
 dist bound (MAPP, 1, O1) (PROA, 233, CE1) kf=50 hi=3
 dist bound (MAPP, 1, O2) (PROA, 233, CE2) kf=50 hi=3
 Info: ***********************************

However, there is no change in the energies or final structure compared to
a minimization without restraints.
I know that this problem has come up in previous threads, e.g.:

But I haven't seen a conclusive answer (although some people hint you still
need PMF lines like " pmf { task = stop time = 25 ps } ", but this is no
solution for minimization).

I really hope someone can shed some light on this matter, as I am desperate
to try out some of these restraints in my NAMD simulations... My only other
option is to use a different package (e.g. CHARMM), but that should not be


Marc van der Kamp, PhD-student
School of Chemistry, Research group of Dr. Adrian Mulholland
University of Bristol
E-mail: Marc.vanderKamp_at_bristol.ac.uk

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:42:46 CST