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

[sudipta]

Hi All,

Thank you very much for your kind reply. But obviously, if I put some
position restraints on membrane then there will be some artifacts.

Also, Chris has mentioned that it is a kind of bug in gromacs. please help
me how do I resolve this issue


sudipta


On Fri, Oct 4, 2013 at 9:33 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
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