Re: Error in PMF Calculations

From: Jeff Comer (
Date: Thu Apr 04 2019 - 07:16:38 CDT

Are you using ABF? At what distance from the sheet is the sampling zero?
How big is your molecule? What does the PMF look like?

My guess is that you have big bulky molecule and it is sterically
restricted from approaching the sheet as closely as you think it should. If
so, this region of the transition coordinate is very high energy and not

Another possibility is that the definition of the transition coordinate (in
terms of atom serial numbers), is not what you think it is.


On Thu, Apr 4, 2019 at 00:23 HEMANTH H 18310019 <>

> Dear all,
> I'm trying to calculate the PMF for the absorption of a molecule on a
> graphene sheet. The calculation is run for 100 ns, but the sampling in the
> region near the sheet is zero or very negligible even after running the
> simulation for an extended time ( ~200 ns). I also tried setting the window
> size to the region that was not being sampled, but that also didn't help.
> Any help in this regard would be highly appreciated.
> --
> *Hemanth H 18310019*
> Research Scholar
> IIT Gandhinagar

Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2019 - 23:20:42 CST