[gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center
Ran Friedman
r.friedman at bioc.uzh.ch
Fri Nov 6 10:57:08 CET 2009
For quite a long time I had the feeling that trjconv doesn't resolve all
situations. Following the very recent discussion between Roland Schutz
and Tsjerk, I'm not sure there is an immediate solution. Ad hoc
approaches such as preparation of tpr files from intermediate snapshots
were useful for me in some cases, so you can try these. For calculations
of distances you can sometimes calculate the shift and apply an a
posteriori fix, but that won't work for visualisation and isn't a robust
solution. I don't think it has anything to do with the MARTINI FF.
Ran.
maria goranovic wrote:
> So lets say that I delete the first frame from the trajectory in which
> some atoms might have been outside the box. Everything should be
> within the box once the simulation starts (from the second frame
> onwards)? So the procedure should work if the reference structure is
> the second frame? I have tried that, and it fails as well.
>
> On Thu, Nov 5, 2009 at 4:40 PM, XAvier Periole <x.periole at rug.nl
> <mailto:x.periole at rug.nl>> wrote:
>
>
> 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
>> <mailto: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 <mailto: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
>>>> <mailto: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 <mailto: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>
>>>> <mailto: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 <http://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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>>>
>>> --
>>> 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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