[gmx-users] trjconv:solute at the center

Nilesh Dhumal ndhumal at andrew.cmu.edu
Mon Oct 17 06:01:42 CEST 2011


I have system with solute is surrounded by 256 solvent molecules. I run
the simulation for 20 ns. I save the snap shot at 500 ps using following

trjconv -f 3.trr -s 3.tpr -n 500-1.ndx -b 500.0 -e 501.0 -dt 1.0 -pbc
nojump -center   -o 500-11.pdb

I tried to keep the solute at the center box. In visualization, the solute
is not at center , its close to box edges.

How can I keep the solute at the center.

I am using Gromacs 4.0.7 version.



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