Hello All. I am simulating t4 lysozyme with NAG. I have added a short peptide label to lysozyme which binds calcium ions.
During the simulation there is some drift. I am attempting to re-center the protein+label+NAG+Ca ion. I am using trjconv and have setup an index file that contains only these atom groups (protein+label+NAG+Ca ion). First, I tried just centering using: trjconv -f d61_15_25ns.gro -s md_initial.tpr -n analysis.ndx -center tric -o test.pdb This center's, however NAG and the calcium ion are not in the expected positions. Using: trjconv -f d61_15_25ns.gro -s md_initial.tpr -n analysis.ndx -center tric -o test.pdb -pbc whole The ions and NAG are where they are expected, however, the protein has been split. Using inbox results in something similar. Does anyone know how to do this? Cheers Mitch _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
