Hi Chris, I've done a gmxdump and there aren't any zeros for any of the LJ values. No capital letter problems either.
Chris Rowan Mon, 27 Jul 2009 12:30:54 -0700 Sounds like your topology/forcefield is incorrect or incomplete. Does your log file from mdrun or the stderr/stdout from grompp/mdrun indicate that you don't have any LJ parameters for some atom types? Try a gmxdump on your .tpr file and inspect the LJ parameters by hand. Are there any zero's where you should have numbers? Perhaps you mixed up some atom types (e.g. with capitilization) or you simply didn't add the necessary values. Chris. -- original message -- Hello, I'm using ffoplsaa with a new atom type (Ag) that I've included in the .atp file, LJ parameters I've specified in the nb file. My system topology I've written by hand in an itp file. The problem is that after any kind of run the molecule penetrates the metal surface! This shouldn't be happening. I had been using g45a3 quite successfully for the same system and everything was working fine. Do I need to do something different/special with oplsaa? What am I missing? Advice appreciated, Chris Rowan _______________________________________________ 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 _______________________________________________ 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