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

[Per Larsson]

Hi,

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
> 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.
>
> -Justin
>
> > 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
> http://www.thelemkullab.com
>
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