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

[Tsjerk Wassenaar]

Hi Ragothaman,

You would do good to try and find out what caused the error. You may
be treating symptoms rather than problems now, and simply covering up
some more severe wrong in your system. Maybe try to start a simulation
after some while, using the same parameters as before. This might
allow your system to relax sufficiently.

Cheers,

Tsjerk

On 1/25/07, Ragothaman Yennamalli <ymr79in at yahoo.co.in> wrote:
> Hi,
> I increased the tau_p to 2.0 and lincs-iter to 4. Now
> the system is running smoothly.
> Regards,
> Ragothaman
>
> --- 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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>
>
>
>
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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