From: MW Van der Kamp, School of Chemistry (Marc.VanderKamp_at_bristol.ac.uk)
Date: Thu Nov 02 2006 - 05:46:21 CST
Hello,
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: FREE ENERGY PERTURBATION CONFIG
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.:
<http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/3041.html>
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
necessary.
Thanks,
Marc
---------------------------------------------------
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
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