On 10/16/19 11:53 AM, Patel, Lara Anne wrote:
Have you tried using the -center flag with -pbc mol for example: gmx trjconv -f traj.xtc -o traj-centered.xtc -center -pbc mol -n index.ndx The reason to give the index file is so that you can select the group that you are centering by. If you do not have the residue's A as a seperate group in the index file, you should start by producing an index file with your centering group isolated and then another group for what you will want to be printing in your new trajectory file. There is one small caveate to the centering algorithm though: There are two ways that the center of mass of an object can be in the middle of the simulation box. 1) The mass is in the center of the box. 2) The mass is split on opposite ends of the box. The last time I was using the -center function of the trjconv function, it would alternate between the two. I am not sure if this has been fixed.
trjconv doesn't choose; it simply computes the center based on coordinates you provide. That's why step 1 in the suggested workflow in the manual is "make molecules whole." That way, there is no issue with placing the atoms in the center.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- 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.
