[gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center
XAvier Periole
x.periole at rug.nl
Thu Nov 5 16:40:37 CET 2009
The nojump option will not apply the pbc when an atom is crossing the
box boundaries ... in your case your bilayer should definitely be in the
center of your box and all the atoms in !!!! If not ot course it does
not work!
On Nov 5, 2009, at 4:33 PM, maria goranovic wrote:
> 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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>>>
>>>
>>> --
>>> Maria G.
>>> Technical University of Denmark
>>> Copenhagen
>>>
>>>
>>>
>>> --
>>> Maria G.
>>> Technical University of Denmark
>>> Copenhagen
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>>
>>
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>>
>>
>> --
>> Maria G.
>> Technical University of Denmark
>> Copenhagen
>> _______________________________________________
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>
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>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
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