[gmx-users] Non-symmetric PMF across lipid bilayer
gmxquestions at gmail.com
Wed Nov 21 13:23:05 CET 2018
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:
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
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