[gmx-users] Can't center box with trjconv

[Erik Marklund]

Try e.g. trjconv -pbc mol -trans ? ? ? to have your molecule not span the edges first. You might also need a trjconv -pbc nojump and trjconv -pbc -mol again afterwards before centering.
 
25 okt 2012 kl. 13.44 skrev Ignacio Fernández Galván:

> I must be doing something wrong, but I can't get trjconv to center the simulation on a residue.
> 
> The simulation box is cubic, the system is formed by an 8-atom frozen molecule and 800 water molecules. I try to center the box with:
> 
>  $ trjconv -f system.cpt -s system.tpr -o conf.gro -center
> 
> (system.cpt and system.tpr are the result of a simulation)
> 
> I select group "2" (the frozen molecule) as a center group, and I get this in the output conf.gro:
> 
>    1ACR     C1    1   0.074   0.042   1.443  0.0000  0.0000  0.0000
>    1ACR     H1    2   0.130   0.139   1.443  0.0000  0.0000  0.0000
>    1ACR      O    3   0.133   2.822   1.443  0.0000  0.0000  0.0000
>    1ACR     C2    4   2.811   0.056   1.443  0.0000  0.0000  0.0000
>    1ACR     H2    5   2.771   0.158   1.443  0.0000  0.0000  0.0000
>    1ACR     C3    6   2.731   2.834   1.443  0.0000  0.0000  0.0000
>    1ACR    H3a    7   2.622   2.843   1.443  0.0000  0.0000  0.0000
>    1ACR    H3b    8   2.775   2.734   1.443  0.0000  0.0000  0.0000
> 
> as you see, the molecule is clearly broken (a difference of more than 2 nm in coordinates), and when visualized, it's indeed in the box's edge.
> 
> I've tried with different combinations of -pdb res/mol, -boxcenter zero/tric/rect, -ur compact, but I always get the molecule broken, sometimes in a corner, sometimes in an edge.
> 
> In case it matters, the initial configuration for the simulation has:
> 
>    1ACR     C1    1   0.138870   0.039109   0.000000
>    1ACR     H1    2   0.195321   0.135855   0.000000
>    1ACR      O    3   0.197788  -0.067044   0.000000
>    1ACR     C2    4  -0.009210   0.052984   0.000000
>    1ACR     H2    5  -0.049761   0.154673   0.000000
>    1ACR     C3    6  -0.089322  -0.054436   0.000000
>    1ACR    H3a    7  -0.198186  -0.045502   0.000000
>    1ACR    H3b    8  -0.045500  -0.154639   0.000000
> 
> and, as I said, this residue (and molecule) is set as frozen, and it is actually frozen during the simulation.
> 
> Is there some bug/limitation in trjconv? Am I doing something wrong?
> 
> Thanks,
> Ignacio
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html