[gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center

[maria goranovic]

Centering on one atom has a problem that the lipid diffuses in the plane of
the membrane, and as a result, the entire system starts to center around the
lipid resulting in a simulation box which translates a lot in the bilayer
plane.

The splitting is not a problem, yes. But during the simulation period when
the bilayer is not split, it diffuses quite a bit along the bilayer normal
(after use of -pbc mol, and centering around the lipid center of mass). a
plot of the lipid center of mass shows the bilayer diffusing along z, when
its not split.

On Thu, Nov 5, 2009 at 2:25 PM, XAvier Periole <x.periole at rug.nl> wrote:

>
> On Nov 5, 2009, at 2:02 PM, Justin A. Lemkul wrote:
>
>
>>
>> maria goranovic wrote:
>>
>>> I did use -pbc nojump, but that does not help
>>>
>>
>> What about entering on a central lipid tail atom, I suggested some time
>> ago? The bilayer probably just splits across periodic boundaries, so this is
>> not really a problem; just a visualization artefact.
>>
> The splitting is not a problem and I think that centering using one lipid
> (tail) won't change the problem if
> the bilayer is cut half! Or the -pbc mol should be applied ...
>
>
>> -Justin
>>
>>  The drift is about 1 nm per 10 microseconds .
>>> (this is a martini simulation)
>>> On Thu, Nov 5, 2009 at 1:02 PM, XAvier Periole <x.periole at rug.nl<mailto:
>>> x.periole at rug.nl>> wrote:
>>>   On Nov 5, 2009, at 12:09 PM, maria goranovic wrote:
>>>       Hello All (and especially Berk)
>>>       This is an update of the problem that I was facing earlier. I
>>>       used to tau_p of 3.0 ps, and the problem does not go away, the
>>>       bilayers still drifts in the simulation box.  So this is
>>>       probably a bug then?
>>>   How much is the drift (nm/ns)? Did you use removal of center of mass
>>>   of the entire system of
>>>   bilayer/solvent separately?
>>>       I still cannot understand how to put the bilayer back into the
>>>       center of the simulation box. As suggested by Justin, I tried to
>>>       use just one tail atom of a lipid for centering, but that did
>>>       not work either.
>>>       I noticed that my bilayer, which is initially at the center of
>>>       the simulation box, separates into two leaflets at the box edges
>>>       from the very first step of the simulation itself, but i am not
>>>       able to correct that using the -center and -boxcenter zero
>>>       options. Can someone please make a suggestion and help?
>>>   You have to do use -pbc nojump first and then center ...
>>>       Thank you so much
>>>       -Maria
>>>       --         Maria G.
>>>       Technical University of Denmark
>>>       Copenhagen
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>>> --
>>> Maria G.
>>> Technical University of Denmark
>>> Copenhagen
>>> ------------------------------------------------------------------------
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>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>
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-- 
Maria G.
Technical University of Denmark
Copenhagen
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