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

[Gmx QA]

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
> >>
> >> ==================================================
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >>
>
> --
> ==================================================
>
> 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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>