Defining custom Colvars to measure pmf with Umbrella Sampling

From: Hemanth Vemuri (
Date: Tue Jun 20 2017 - 00:25:29 CDT

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
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

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