Hi Nayef, >> grompp –f em.mdp –c fws_b4em.gro –p fws.top –o fws_em.tpr >> genion –s fws_em.tpr –o fws_ion.gro –nname CL- –nn 2 –g fws_ion.log >> [select Group 12: SOL] >> pico fws.top [reduce number of SOL by two and add 2 CL- at the end of the >> file]
This is all fine. You take the structure before em, make a run input file from it to run genion, adding some ions. You update the topology file, which seems sensible. But then, mind you that the file with the ions is fws_ion.gro. That file you should process with the edited topology to form a run input file for EM. Now look what you're doing here: >> mdrun –s fws_em.tpr –o fws_em.trr –c fws_b4pr.gro –g em.log –e em.edr & Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- 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
