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

[Gmx QA]

Hi Sheryas,

Thanks - so are you saying that the PMF should be asymmetric with respect
to the leaflets even before I make the PMF symmetric? This seems to
contradict what Justin just said, but maybe you mean the same thing?

Den ons 21 nov. 2018 kl 14:57 skrev Shreyas Kaptan <shreyaskaptan at gmail.com
>:

> I am reasonably sure that if the bilayer composition is asymmetric with
> respect to leaflets you should see asymmetry in the PMF. In the ideal case,
> of infinite sampling, you should have zero free energy difference in the
> bulk solvent for either side.
>
> On Wed, Nov 21, 2018 at 2:52 PM Gmx QA <gmxquestions at gmail.com> wrote:
>
> > Thanks again,
> >
> > So then to summarize: Using -sym is appropriate in this case, even though
> > the bilayer is asymmetric with respect to lipid composition.  This fact
> > would show up anyway (in the limit of unlimited sampling?)
> >
> >
> >
> > Den ons 21 nov. 2018 kl 14:44 skrev Justin Lemkul <jalemkul at vt.edu>:
> >
> > >
> > >
> > > On 11/21/18 8:39 AM, Per Larsson wrote:
> > > > 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?
> > >
> > > No, because that's completely unknown (and irrelevant) to WHAM. It sets
> > > the leftmost window to a zero energy and calculates every window's
> > > energy relative to that, so you'll get the steady increase you see. If
> > > you tell it that the leftmost and rightmost windows are equal (which
> > > -sym), then the calculation proceeds differently.
> > >
> > > -Justin
> > >
> > > >
> > > >
> > > >
> > > > 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
> > > >> 340 West Campus Dr.
> > > >> Blacksburg, VA 24061
> > > >>
> > > >> jalemkul at vt.edu | (540) 231-3129
> > > >> http://www.thelemkullab.com
> > > >>
> > > >> ==================================================
> > > >>
> > > >> --
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> > >
> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Assistant Professor
> > > Office: 301 Fralin Hall
> > > Lab: 303 Engel Hall
> > >
> > > Virginia Tech Department of Biochemistry
> > > 340 West Campus Dr.
> > > Blacksburg, VA 24061
> > >
> > > jalemkul at vt.edu | (540) 231-3129
> > > http://www.thelemkullab.com
> > >
> > > ==================================================
> > >
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>
> --
> Shreyas Sanjay Kaptan
> --
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