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

[Ragothaman Yennamalli]

Hi Mark,
Thanks for the mail. Yes, I solvate the protein and
then do a EM with steepest descent and then I proceed
to do position restrained MD, first restraining the
protein and then the backbone. It is at the backbone
restraint step I got this error. Also I assumed that
if there are any bad contacts they would get resolved
in minimization step, but looks like it hasn't. Please
tell me how to solve this problem. 
Raghu
--- Mark Abraham <Mark.Abraham at anu.edu.au> 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
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