On 10/6/12 4:08 AM, Albert wrote:
hello:
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.
No, it is not. A periodic system has no center, and the centering algorithm is
merely a convenience for visualization.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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