[gmx-users] Membrane is shifted a lot during umbrella sampling

Justin Lemkul 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

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Justin A. Lemkul, Ph.D.
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