[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 13:14:47 CET 2009

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
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