[gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center
maria goranovic
mariagoranovic at gmail.com
Thu Nov 5 16:33:23 CET 2009
my starting structure looks quite all right to me. everything is in the box
(except the tails of some lipids) .. wonder whats wrong. thank you verymuch
for helping
On Thu, Nov 5, 2009 at 4:04 PM, XAvier Periole <x.periole at rug.nl> wrote:
>
> On Nov 5, 2009, at 4:00 PM, maria goranovic wrote:
>
> Hi Xavier,
>
> Thanks for the clear instructions. The bilayer is not in one piece in the z
> direction after the -pbc nojump for some reason.
>
> the problem might be from your starting structure, everything should be in
> the box!
> Or you may be facing strange/funny/incomprehensible behavior ...
>
>
> after the third step, the water is in the right place, but the bilayer has
> expanded to periodic boxes in the xy plane. so the center of mass of the
> lipid molecules is not really being centered in the box ?
>
>
> On Thu, Nov 5, 2009 at 3:34 PM, XAvier Periole <x.periole at rug.nl> wrote:
>
>>
>> you need to do:
>>
>> 1- trjconv -pbc nojump; this keeps your bilayer in one piece on the z
>> direction
>> 2- trjconv -center; using the bilayer to center and the system as output;
>> this will
>> translate your bilayer on the z axis and normally not modify it on the xy
>> plan.
>> 3- trjconv -pbc mol; will put your lipids in one piece in the box; I
>> believe this
>> step cn be coupled to the previous quite safely.
>>
>> On Nov 5, 2009, at 3:23 PM, maria goranovic wrote:
>>
>> 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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>
>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
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--
Maria G.
Technical University of Denmark
Copenhagen
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