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

[Tsjerk Wassenaar]

Salut Xavier,

Hmm, illustrating again that it pays off sometimes to spend a few more
moments thinking about things before writing something. You're right
again. Removel of jumps is performed before centering, but, for the
next frame, the centered system will be used to remove the jumps. So
that's bound to give garbled results for anything but the first frame.
Solution: store the shift that is applied and use it when determining
whether atoms jumped...

Cheers,

Tsjerk

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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-- 
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