[gmx-users] Non-symmetric PMF across lipid bilayer
jalemkul at vt.edu
Wed Nov 21 14:44:04 CET 2018
On 11/21/18 8:39 AM, Per Larsson wrote:
> 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.
> 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:
>> 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.
>> 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
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Justin A. Lemkul, Ph.D.
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
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