[gmx-users] Non-symmetric PMF across lipid bilayer

Justin Lemkul jalemkul at vt.edu
Wed Nov 21 14:24:41 CET 2018

On 11/21/18 7:22 AM, Gmx QA wrote:
> Hi all gmx-users
> I am working on calculating the PMF using umbrella sampling of a (rather
> large) molecule across a lipid bilayer. I have set up my umbrellas with a
> 0,2 nm spacing, and run each window for 100 ns.
> The problem is that the resulting PMF is not symmetric with respect to the
> bilayer center. Initially is looks ok, but when the molecule is exiting the
> bilayer on the other side again, the PMF does not go back to (roughly) the
> same value as before entering the bilayer.
> I have uploaded the PMF file here:
> https://files.fm/u/7ec2rshc

You didn't get a symmetric profile because you didn't ask for one. Use 
the -sym option.


> Any comments or suggestions are much appreciated. I understand the problems
> and issues about calculations of a converged PMF with larger molecules, but
> nevertheless I would have expected my PMF to be symmetric, albeit perhaps
> not converged.
> Thanks
> /PK


Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129


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