[gmx-users] how to center the molecule with trjconv

Zhenyu Meng fdmm1989 at gmail.com
Wed Jul 15 05:20:03 CEST 2015

Dear GROMACS users,
I want to simulate DNA in a cubic box with water as solvent and visualize
By using -pbc mol I can see part of the DNA is out of the box so I want to
center the DNA in box.
But using -center seems destruct the DNA into several parts. I tried to use
-pbc mol followed by -center or -center followed by -pbc mol but both
cannot center the DNA (the DNA doesn't fall apart but it's still not in the
I'm curious about the algorithm about -center option. e.g. if I have a pbc
cubic box with length of 5, and the COM of the DNA is at (3,3,3), in that
way, if I use -center I think all the atoms of the system(including DNA and
water) will shift with a vector(-0.5,-0.5,-0.5) to make sure the COM of DNA
is now at(2.5,2.5,2.5) (the default boxcenter). Am I correct?
Your help will be highly appreciated!

Mr. Meng Zhenyu
Division of Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University

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