Hi, I increased the tau_p to 2.0 and lincs-iter to 4. Now the system is running smoothly. Regards, Ragothaman
--- Mark Abraham <[EMAIL PROTECTED]> wrote: > Ragothaman Yennamalli wrote: > > HI, > > Since the log files and crashed .pdb files had > filled > > the whole disk space I had to delete them and > start > > again. > > I am simulating a homodimer protein in a water > box. I > > have mutated three residues and want to look the > > behaviour of the protein. I have four setups for > the > > same protein without mutation and with mutation > and > > respective controls. Among the four only one is > > crashing at the position restraint stage. The > other > > three didnt show me this error (except for the one > > line LINCS warning). > > I have run the position restrained dynamics again. > Yes > > as you are saying it starts with LINCS warning. > > This is what it says after the LINCS warning. > > You should be doing some energy minimization before > attempting MD, else > some bad contacts will send badness around the > system, maybe eventually > causing such crashes. Make sure you do EM after > solvating (and before if > you need to!) > > Mark > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 > __________________________________________________________ Yahoo! India Answers: Share what you know. Learn something new http://in.answers.yahoo.com/ _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
