[gmx-users] how to center to molecule in pbc box?

Albert mailmd2011 at gmail.com
Sat Oct 6 10:08:50 CEST 2012


I am using the following command for md production in gromacs:

grompp -f md.mdp -p md.top -o md.tpr

mpirun -np 64 mdrun -s md.tpr -x md.xtc -g md.log

However, I found that the md.xtc file need command:

trjconv -f md.xtc -o convert.xtc -pbc mol

to put the molecule in the centre of pbc box, otherwise it is messy when 
we visualize in VMD. I am wondering, is it possible to ask mdrun 
generate the .xtc file cetering the molecule in PBC box automatically 
and we no longer need to use trjconv command to convert it.

thank you very much

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