Re: Defining custom Colvars to measure pmf with Umbrella Sampling

From: Radak, Brian K (
Date: Wed Jun 21 2017 - 11:01:08 CDT

Giacomo's response is definitely the more relevant for setting up simulations.

I'll just add that it does not seem to be widely appreciated that reweighting methods such as (binless) WHAM do not require that the PMF be computed along the colvar that experiences a bias -- any colvar can be used. This is not widely implemented, but can be done fairly straightforwardly.

Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory

9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643
From: <> on behalf of Giacomo Fiorin <>
Sent: Tuesday, June 20, 2017 9:49:26 PM
To: NAMD list; Hemanth Vemuri
Subject: Re: namd-l: Defining custom Colvars to measure pmf with Umbrella Sampling

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--_000_CY4PR09MB12380BC9473233B0E9FEF981D6DA0CY4PR09MB1238namp_--

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