[gmx-users] Membrane is shifted a lot during umbrella sampling
chris.neale at mail.utoronto.ca
Fri Oct 4 16:32:33 CEST 2013
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). 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).
-- original message --
I am facing problem for doing umbrella sampling simulation for the
transferring of a small peptide across a membrene in presence of electric
field. Moreover, the simulation was carried out at constant area. Martini
force field for protein, lipid and water was used for this simulation. The
electric field was applied along the -z direction across the membrane. The
problem, which I am facing is that the position of membrane is shifted a
lot during this this simulation. Moreover, I notice the shifting of
membrane is significantly enhanced when I apply high electric filed. I
don't have any clue for this shifting problem. If anyone have idea to
arrest the shifting problem then please share it. A copy of my input file
is attached herewith.
Thanks in advance
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