[gmx-users] MPIRUN error while running position restrained MD

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jan 23 06:13:56 CET 2007

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!)


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