Re: A problem in ABF simulations

From: Jeff Comer (
Date: Mon Nov 24 2014 - 11:44:45 CST

How is your collective variable defined? The center of mass distance
between the two ions?


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

On Sat, Nov 22, 2014 at 5:50 AM, Azadeh Alavi <> wrote:
> Dear NAMD users,
> I have a system of membrane-protein and intend to do ABF simulations. In one
> of the windows the positive ion is attracted to the negative residues and
> stick to them till the end of the simulation, although I have increased the
> cutoff and continued the simulation for more nanoseconds. Therefore, only
> half of the window is sampled and half of the data in the '.count' file is
> 0.
> Your help would be greatly appreciated. Thanks a lot.
> Regards,
> Azadeh

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