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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