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

[XAvier Periole]

On Nov 6, 2009, at 1:21 PM, maria goranovic wrote:

> 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?
That is fine, you care only of the z direction here :)).

is it finally working ?

>
> -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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