Re: Defining custom Colvars to measure pmf with Umbrella Sampling

From: Vermaas, Joshua (
Date: Wed Jun 21 2017 - 11:06:57 CDT

As an approximation, something like the contacts (coordnum) between protein heavy atoms and water heavy atoms will give the same sort of flavor as the number of intercalated waters. There will be a reasonably consistent "shell" term of protein water contacts you can't do anything about, but depending on the protein configuration, the number of waters within your protein would change by a measurable amount.


On 06/20/2017 08:56 PM, Giacomo Fiorin wrote:
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:
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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