Hi Vivek, > Now when I am processing the modified .gro file to generate box, the ligand > and cofactor are going away from the protein molecule and I am not able to > analyze the complex.
Gradually going away, or suddenly jumping? In the latter case, read up on periodic boundary conditions. Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
