Hi All, I am trying to simulate kinase domain (chain A) in complex with cyclin (chain B). During solvent dynamics, PBC on and PME treatment of electrostatics, i need to keep only kinase domain flexible but cyclin fixed.
i put POSRES_B in define variable and tried to simulated the entire solvated system in GROMACS 4 package. But time and again it failed with LINCS warnings. On the contrary, if entire system is kept either flexible or position restrained, run is obtained without any errors. I tried 1ns MD. Unable to understand possible reasons. Could anybody help in this regard ? Regards, Nikhil
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
