[gmx-users] how to center a MARTINI trajectory so that the lipid bilayer remains at the center of the box

[XAvier Periole]

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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