[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 16:04:52 CET 2009


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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