[gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center
XAvier Periole
x.periole at rug.nl
Fri Nov 6 10:55:04 CET 2009
Lets make it clear. I can not tell you if the atoms in the second
frame are in the
box or not! You have to visualize it!
Honestly it is not in the first frame I can not see how it would in
the second!
You have to build a reference structure that has the bilayer in one
piece, then
the nojump option can actually to the job you want.
On Nov 6, 2009, at 10:37 AM, 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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>>>> --
>>>> 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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>
>
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>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
> _______________________________________________
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