Re: Defining custom Colvars to measure pmf with Umbrella Sampling

From: Radak, Brian K (
Date: Wed Jun 21 2017 - 11:16:49 CDT

This does not make sense to me - there is very much a collective variable to describe the number of waters as a reaction coordinate - you just count the number of waters that meet your criterion. Whether or not you can apply a bias to this coordinate is a different question, but this does not seem to be what you are asking.

Your question seems more related to analysis than simulation setup using NAMD or colvars. Am I misunderstanding?

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 Hemanth Vemuri <>
Sent: Tuesday, June 20, 2017 12:25:29 AM
Subject: namd-l: Defining custom Colvars to measure pmf with Umbrella Sampling

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_CY4PR09MB12382BA41CEBD1E7553B0D14D6DA0CY4PR09MB1238namp_--

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