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

[Tsjerk Wassenaar]

Hi Maria,

If you want to keep your lipid molecules whole, some parts will indeed
be sticking out in the xy-plane. But that's okay.

Cheers,

Tsjerk

On Fri, Nov 6, 2009 at 1:21 PM, maria goranovic
<mariagoranovic at gmail.com> 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?
>
> -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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-- 
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