Hi all I have done MD job on a 226 residue protein with cubic box -d 0.9 in the editconf step. after 30 ns I entered the last step pdb to the simulating annealing, again with cubic box and -d 0.9. the highest temp was 600 K and the loest was 50 K. When I see the pdb of structures at 300 K, 600 K and 50 K in pymol, it seems the structures converts to 2 part, one along oneside of cubic's surface the other was in the parallel side, I mean that the system move out of the cubic, and the outer part appears in another side of cubic, so I dont have the integrate structure. How can I fix this problem.
Thank you in advance for your help. -- Tehran University of Medical Sciences www.tums.ac.ir -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. _______________________________________________ gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
