[gmx-users] gmx trjconv -center not working?

Mala L Radhakrishnan mradhakr at wellesley.edu
Tue Feb 5 17:38:11 CET 2019


I am trying to extract snapshots and center on a particular group, but the
center of the box does not correspond to the geometric center of the group
as expected.  It is centered on the outer edge of the group.  Here is the
command I am using:

gmx trjconv -f md.xtc -o md_201000ps.pdb -s md.tpr -b 201000 -e 201000 -n
INDEX.ndx -center

...and I then choose the group in the index file that corresponds to what I
want right in the center; I have verified the correctness of the index
file.  I ran my simulation with pbc but in this case I specifically want to
maintain the same cubic box used in the simulations, so I don't want to
keep molecules whole.  So all I want to do is extract the cubic box that is
centered on the group I want.   But the resulting snapshot has the molecule
slightly (about 10%) off center, mainly in the y direction in this case.  I
presume that center will place the geometric center of the group you choose
at the geometric center of the box.  Am I incorrect?  Is there another way
to accomplish what I want?

Thank you so much,


Mala L. Radhakrishnan
Whitehead Associate Professor of Critical Thought
Associate Professor of Chemistry
Wellesley College
106 Central Street
Wellesley, MA 02481

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