[gmx-users] Membrane is shifted a lot during umbrella sampling
jalemkul at vt.edu
Sat Oct 5 03:33:00 CEST 2013
On 10/4/13 10:32 AM, Christopher Neale wrote:
> Dear Sudipta:
> on average, bilayers migrate along the positive z axis during gromacs
> simulations with a variety of atomistic force fields. This has been reported
> before, but never fully resolved ( http://redmine.gromacs.org/issues/165
> suggests it is due to rounding ) and I see it all the time. It is not that
> rapid, but in microsecond-scale simulations it is quite obvious and
> statistically significant (i.e., we're not talking about something I've seen
> in one simulation ... the chance that this "upward" drift is due to random
> noise that could lead to drift along plus or minus z are vanishingly small).
FWIW, I recall the same effect being reported for CG force fields not too long ago.
> I presume that an electric field could magnify this incorrect behaviour. That
> said, if your membrane has a net charge, or contains an embedded protein with
> a net charge, then I expect that migration along the applied field is
> actually the proper behaviour.
> There are a few ways that you could stop drift along the z axis. One is to
> use the pull code to restrain your bilayer COM to (0,0,0) or some other
> absolute position (i.e., no reference group selected in the pull code) and
> only turn on the Z component of the pull force. You could also set comm-grps
> to remove COM motion of the bilayer only (hopefully somebody else will let me
> know if that is a bad idea for some reason).
That sounds suspicious to me. I think you'd end up with artifacts, not the
least of which would be the bilayer potentially crashing into water molecules.
Justin A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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