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

[maria goranovic]

One more note about -pbc nojump. I typically use -pbc mol. Using pbc nojump
succeeds in keeping the center of the bilayer at 0 0 0, but the atoms have
moved way out of the simulation box resulting in a dilute system

On Thu, Nov 5, 2009 at 2:31 PM, maria goranovic <mariagoranovic at gmail.com>wrote:

> 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
>



-- 
Maria G.
Technical University of Denmark
Copenhagen
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