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

[sudipta]

Hi Chris,

The lipid of my system is DPPC, which is a neutral. However, the peptide is
positively charged polyarginine. The membrane is shifted a lot when the
peptide is embedded within it (i,e peptide restrained at the bilayer
region). Therefore presence of peptide inside the membrane produces such
migration in presence of electric field. Although, it is physically
meaningful, but do you think calculation of potential of mean force of such
system in presence of electric field is meaningful. I am not quite sure
about this.

Sudipta



On Fri, Oct 4, 2013 at 10:32 AM, Christopher Neale <
chris.neale at mail.utoronto.ca> 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). 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).
>
> Chris.
>
> -- 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
> Sudipta
>
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