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 gmx-users@gromacs.org
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
