Using colvars for biasing potential in Umbrella Sampling

From: begüm alaybeyoğlu (
Date: Wed Jan 07 2015 - 10:01:17 CST

Dear NAMD users,
I'm trying to run umbrella sampling simulations for membrane translocation
of a peptide. I have already run SMD simulations for this system and im
getting my conformations from SMD simulations to be used as initial
conformation in each umbrella window. My problem is that I want to bias the
z coordinate of the SMD atom, since my pulling direction is z (from
positive z values to negative, according to my system) and i have chosen z
coordinate as my reaction coordinate. I know i can use colvars for this,
but not quite sure how to define it. I'm thinking that I can define
harmonic restraints on the distance between the membrane core and SMD atom,
but can it be applied only on the z coordinate? Does "distanceZ" colvar
definition satisfy this or does it compute the distance (in x, y, z) and
project on z axis? Any help is appreciated.



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