Hi, 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 -- Mala L. Radhakrishnan Whitehead Associate Professor of Critical Thought Associate Professor of Chemistry Wellesley College 106 Central Street Wellesley, MA 02481 (781)283-2981 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
