[gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center
Tsjerk Wassenaar
tsjerkw at gmail.com
Fri Nov 6 11:44:26 CET 2009
Hi,
Following this discussion for the past days or so, let's first make
one thing clear: -pbc nojump is of no use at all when the purpose is
to keep things together. That only works if everything moves together
and there is no diffusion, like in protein complexes. For solvent, and
for bilayers, applying -pbc nojump will actually reveal the diffusion
across boxes, countering the wrapping that would otherwise occur in
mdrun (for mathematical/computational reasons). I hope that settles
that part of the discussion.
Now the problem here is that the membrane drifts, and the purpose is
to remove that drift. If it would only be required that the leaflets
stayed together, that could actually be achieved by removing jumps
only in the membrane normal direction. So that would call for options
like -pbc nojump_x | nojump_y | nojump_z That's actually not that
hard to do. Applying such a procedure followed by centering might
actually come close to what Maria wants to do. The other option is to
calculate the change in COM from the displacements of particles in the
periodic system, rather than from the actual COM. Compensating for
such a shift and then putting all atoms back in the box I think would
be the solution to the problem. That would call for an option like
-fit com, that could be used together with pbc options (-pbc nojump |
inbox | ... ). If required I may be able to implement such changes, or
provide the routine.
Cheers,
Tsjerk
On Fri, Nov 6, 2009 at 10:57 AM, Ran Friedman <r.friedman at bioc.uzh.ch> wrote:
> 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> 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> 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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>>>>>>>> _______________________________________________
>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
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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
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>>
>>
>>
>> --
>> Maria G.
>> Technical University of Denmark
>> Copenhagen
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>
>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
>
> ________________________________
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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