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
--
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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