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

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Nov 6 12:55:47 CET 2009

Cher Xavier,

> 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

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.



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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