On 5/2/19 6:59 AM, Saumyak Mukherjee wrote:
Dear All, I have an insulin hexamer, which (because of PBC) apparently breaks into pieces after simulation. To make the molecule whole, I use the following command: gmx trjconv -f traj.xtc -s md.tpr -o traj_whole.xtc -pbc cluster or gmx trjconv -f traj.xtc -s md.tpr -o traj_whole.xtc -pbc mol -ur compact This command(s) makes each chain (out of the 6) whole, but the chains do not come together. So the hexamer as a whole still remains broken. Is there a way to solve this problem?
Use -center with an index group corresponding to residues that constitute the interface of one protein.
-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.
