[gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center

[maria goranovic]

Thanks for the nice discussion.

Xavier, when you say that the reference structure should have the bilayer in
the center of the box, and everything inside the box, are you referring to
all three dimensions? My reference structure does have the bilayer at the
box center, but some lipid tails will always point out of the box in the xy
plane, would they not?

-Maria

On Fri, Nov 6, 2009 at 1:14 PM, XAvier Periole <x.periole at rug.nl> wrote:

> Best Tsjerk,
>
>
>  Well you can see the bilayer as protein complex where each monomer is
>>> a leaflet. Applying -pbc nojump on the trajectory would simply keep the
>>> two
>>> leaflets together. Then the system can be centered using the bilayer as
>>> reference: this would put the bilayer at the center of the z axis. The
>>> movements
>>> "out of the box" can then be corrected using -pbc mol.
>>> It is trivial is the reference structures are correct.
>>>
>>
>> Ah, my imagination got stuck a bit... Yes, that would work. And
>> removal of jumps is applied before centering, so these can be combined
>> in one command. That would make:
>>
>> trjconv -center -pbc nojump
>> trjconv -pbc mol
>>
>>  Actually I believe the mixing nojump and centering never worked for me!
> I generally do a trial first :))
>
>
>  That may be the quickest work-around and should indeed solve the COM
>> trend in the z-direction. But it may give COM jitter or COM trend in
>> the (xy) plane.
>>
>> Groetjes,
>>
>> Tsjerk
>>
>> --
>> 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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-- 
Maria G.
Technical University of Denmark
Copenhagen
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