Re: Defining custom Colvars to measure pmf with Umbrella Sampling

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
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.

Giacomo

http://www.pnas.org/content/112/27/8181

On Tue, Jun 20, 2017 at 1:25 AM, Hemanth Vemuri <hemanthvemuri1997_at_gmail.com
> 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
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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