[gmx-users] Non-symmetric PMF across lipid bilayer
larsson.r.per at gmail.com
Wed Nov 21 14:39:14 CET 2018
Thanks Justin, but shouldn't the PMF be (more or less) symmetric anyway,
given the inherent bilayer symmetry?
In this case I have designed the two leaflets in the bilayer to have
non-identical lipid composition, so then I think using -sym would
obliterate any differences between the leaflets, no?
On Wed, Nov 21, 2018 at 2:24 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
> > bilayer center. Initially is looks ok, but when the molecule is exiting
> > bilayer on the other side again, the PMF does not go back to (roughly)
> > 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
> > and issues about calculations of a converged PMF with larger molecules,
> > 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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