Re: Defining custom Colvars to measure pmf with Umbrella Sampling

From: Giacomo Fiorin (
Date: Tue Jun 20 2017 - 21:49:26 CDT

Hello Hemanth, this is not a trivial problem, because your definition makes
sense for analysis (it is pretty much a VMD selection) but in dynamics you
need to use continuous forces.

There are a few approaches to this (see e.g. one below), but first you have
to ask yourself what is the role of protein flexibility in your problem.


On Tue, Jun 20, 2017 at 1:25 AM, Hemanth Vemuri <
> wrote:

> Hello,
> My goal is to measure the changes in pmf as we vary the number of water
> molecules inside/around(1) a protein. But the problem i am facing is that
> there is no suitable colvars which will help me achieve this, like for
> example if i want to measure pmf with radius of gyration as the reaction
> coordinate , there is already Rg collective variable which i can specify
> in the colvars input file, but there is no colvar with which i can measure
> the pmf with number of water as a reaction coordindate. Hence i wanted to
> know if there is a way with which i can define a custom collective variable
> or is there any other way to reach my goal.
> (1) - I call these waters as penetrated waters and am defining them as
> waters belonging to contact water which are not within 3 angstrom of bulk
> water.
> Contact water are defined as water within 3.5 angstrom of protein and the
> water which are not contact water are defined as bulk water.
> Thanks for advice
> Hemanth Vemuri,
> undergraduate student
> Center for Computational Natural Sciences and Bioinformatics,
> International Institute of Information Technology,
> Gachibowli, Hyderabad 500 032
> Telangana, India

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD

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