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

[Ragothaman Yennamalli]

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.
*****************
Back Off! I just backed up step20672.pdb to
./#step20672.pdb.1#
Sorry couldn't backup step20672.pdb to
./#step20672.pdb.1#
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates

Step 20673  Warning: pressure scaling more than 1%,
mu: 8.9983e+20 8.9983e+20 8.9983e+20

Step 20673  Warning: pressure scaling more than 1%,
mu: 8.9983e+20 8.9983e+20 8.9983e+20

Step 20673  Warning: pressure scaling more than 1%,
mu: 8.9983e+20 8.9983e+20 8.9983e+20

Step 20673  Warning: pressure scaling more than 1%,
mu: 8.9983e+20 8.9983e+20 8.9983e+20

Step 20673, time 91.346 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 348017441898496.000000 (between atoms 7000 and
7002) rms nan
bonds that rotated more than 30 degrees:
******************
I am attaching the .mdp file along with this email. 
Thanks in advance.
Raghu

--- Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Ragu,
> 
> The tail of the .log file is not very informative
> here. Please try to
> find in the log where it first went wrong. It may
> well start out with
> a LINCS warning.
> Besides, please be more specific in what you're
> trying to simulate,
> and what protocol you used.
> 
> Cheers,
> 
> Tsjerk
> 
> On 1/19/07, Ragothaman Yennamalli
> <ymr79in at yahoo.co.in> wrote:
> > Hi,
> > This is the tail of the .log file
> > new box (3x3):
> >    new box[    0]={-4.13207e+15,  0.00000e+00,
> > -0.00000e+00}
> >    new box[    1]={ 0.00000e+00, -5.17576e+15,
> > -0.00000e+00}
> >    new box[    2]={ 0.00000e+00,  1.51116e+23,
> > -1.14219e+16}
> > Correcting invalid box:
> > old box (3x3):
> >    old box[    0]={-4.13207e+15,  0.00000e+00,
> > -0.00000e+00}
> >    old box[    1]={ 0.00000e+00, -5.17576e+15,
> > -0.00000e+00}
> >    old box[    2]={ 0.00000e+00,  1.51116e+23,
> > -1.14219e+16}
> > THe log files have generated as huge files (approx
> > 20GB) which have used all the disk space.
> > Raghu
> > --- Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> >
> > > Ragothaman Yennamalli wrote:
> > > > Dear all,
> > > > I am running gromacs3.2 version. When I am
> running
> > > the
> > > > position restraint md for the protein, the
> process
> > > > stops within 100 steps with the following
> error:
> > > >
> > >
> >
>
-----------------------------------------------------------------------------
> > > > One of the processes started by mpirun has
> exited
> > > with
> > > >       nonzero exit
> > > > code.  This typically indicates that the
> process
> > > > finished in error.
> > > > If your process did not finish in error, be
> sure
> > > to
> > > > include a "return
> > > > 0" or "exit(0)" in your C code before exiting
> the
> > > > application.
> > > >
> > > > PID 16200 failed on node n0 (10.10.0.8) due to
> > > signal
> > > > 9.
> > > >
> > >
> >
>
-----------------------------------------------------------------------------
> > > >
> > > > I searched the mailing list and google and
> > > understood
> > > > that the pressure coupling parameter "tau_p"
> value
> > > in
> > > > the .mdp file has to be more than 1.0 and I
> did
> > > the
> > > > same.
> > >
> > > This is likely irrelevant. What do the ends of
> the
> > > .log files say?
> > >
> > > Mark
> > > _______________________________________________
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> >
> >
> >
> >
> >
>
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> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
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