Re: Using colvars for biasing potential in Umbrella Sampling

From: Giacomo Fiorin (
Date: Wed Jan 07 2015 - 10:08:11 CST

Yes, that's the definition of distanceZ.


On Wed, Jan 7, 2015 at 11:01 AM, begüm alaybeyoğlu <>

> 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.
> Thanks!
> Begüm

Giacomo Fiorin
Assistant Professor of Research
Institute for Computational Molecular Science (ICMS)
College of Science and Technology, Temple University
1925 North 12th Street (035-07), Room 704D
Philadelphia, PA 19122-1801
Phone: +1-215-204-4213

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