Hi List, 1) I m running a drug -enzyme simulation. I ran 62 ps of simulated annealing followed by production runs of 5ns usng NPT and PBC and PME.. After 5ns, the protein moves far away from the ligand. I checked the 4ns gro files, the ligand and protein are bound together, but its only that 5ns gives issues.
2) I ran another similar but smaller system and the complex is stable even after 8ns. What went wrong with the simulations in case 1? Is there a way to fix this problem? Your help is much appreciated. Regards, Neha Gandhi, School of Biomedical Sciences, Curtin University of Technology, GPO Box U1987 Perth, Western Australia 6845 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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
