[gmx-users] Re: how to center a MARTINI trajectory so that the lipid bilayer remains at the center of the box (XAvier Periole)

[Nicolas SAPAY]

I remember having a similar issue a long time ago. If I remember
correctly, the culprit was a bad parametrization of the Langevin piston.
Maybe you should specified how the pressure is controlled, as well as how
you managed the center of mass motions in you dynamics.

Nicolas


> Well the bilayer drifts down in the z-direction, and eventually the
> leaflets
> almost separate, with each leaflet being on opposite ends of the box.
>
> if i try pbc nojump, the lipids drift far away from the box  in the xy
> plane
>
> On Fri, Jul 3, 2009 at 12:00 PM, <gmx-users-request at gromacs.org> wrote:
>
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>>   1. Re: how to center a MARTINI trajectory so that the lipid
>>      bilayer remains at the center of the box (XAvier Periole)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Fri, 3 Jul 2009 11:43:55 +0200
>> From: XAvier Periole <x.periole at rug.nl>
>> Subject: Re: [gmx-users] how to center a MARTINI trajectory so that
>>        the lipid       bilayer remains at the center of the box
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <EEA7DAA1-6584-4AF0-8321-3FEA30A413F4 at rug.nl>
>> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>>
>>
>> What is the problem exactly? The two layers separate over the pbc?
>> did you try a -pbc nojump prior the centering?
>>
>> On Jul 3, 2009, at 11:37 AM, maria goranovic wrote:
>>
>> > Dear All,
>> >
>> > This has been discussed before for individual frames. But I am
>> > having a problem in trying to center a trajectory so that the
>> > bilayer remains at the center of the box. I have tried several
>> > combinations, but none of the them work. In each case, the centering
>> > and/or the fitting is done on the lipid bilayer itself.
>> >
>> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
>> > center -boxcenter zero -pbc mol
>> >
>> > this one works for one particular .gro file, but not for the whole
>> > trajectory. I tried all of the following, but none of them work.
>> > What is the solution ?
>> >
>> >
>> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
>> > center -boxcenter zero
>> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -pbc
>> > mol -boxcenter zero
>> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -pbc
>> > mol -center
>> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx   -
>> > pbc mol -fit trans
>> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx   -
>> > pbc mol -fit trans -center
>> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx   -
>> > pbc mol -fit trans -center -boxcenter zero
>> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -fit
>> > trans
>> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -fit
>> > progressive
>> >
>> > --
>> > Maria G.
>> > Technical University of Denmark
>> > Copenhagen
>> > _______________________________________________
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>
>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
> _______________________________________________
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