Re: Query regarding ABF Tutorial on Methane Hydration

From: Chris Chipot (
Date: Thu Jun 24 2010 - 18:23:43 CDT

Dear Navendu,

> As per your last mail, I performed minimization, heating and
> equilibration of the Methane-water system in NPT ensemble (did not
> increase the z-dimension basis vector to 60.)
> This was followed by ABF calculation (increased the z-dim to 60. for
> gas phase) in the NVT ensemble using the .conf file provided in the
> tutorial. The lower and upper wall boundaries
> were set to 0 A and 25 A respectively (files attached). Following
> are the issues/observations from the simulation data :
> 1. Even after equilibration in the NPT ensemble, there is still
> significant box shrinkage in the xy plane.

More than likely because your cubic water box was not properly

> 2. PMF profile (extracted from data in .pmf file) does not match the
> one in tutorial.

For the simple reason that you are using a reaction coordinate
that spans the entire, 25-┼ pathway.

There is a rationale for recommending in the tutorial to break
the reaction pathway in five non-overlapping 5-┼ windows.

> 3. The lowest PMF value is 0. Should'nt it be negative as in the
> tutorial ?

A free energy is defined up to an integration constant.

> 4. I came across a ABF topic in NAMD forum
> (
> where Dr. Fiorin mentioned that lower and upper wall boundaries need
> to have -ve and +ve values for distanceZ component.
> However, in this tutorial, the values range from 0 to 25 A ?

If the center of mass of your water lamella is (0,0,0), then
your lower and upper bounds should be 0 and 5 ┼ (if you split
your reaction pathway into windows), 5 and 10 ┼, ..., 20 and
25 ┼.

Please, read the text of the tutorial carefully.

Chris Chipot


Chris Chipot, Ph.D.
on leave from Nancy UniversitÚ, CNRS
Theoretical and Computational Biophysics Group
Beckman Institute
University of Illinois at Urbana-Champaign
405 North Mathews Phone: (217) 244-5711
Urbana, Illinois 61801 Fax: (217) 244-6078


The light shines in the darkness, and the darkness has not overcome it.

                                                               John 1:5.

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