[gmx-users] my big problem

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Mar 29 10:33:39 CEST 2007

Hi Ozge, Mark,

Mark is of course completely right regarding the MPI error.., you're
messing up something. Where was my mind? Sharp peaks in the RMSD and
radius of gyration plots may indicate jumps over the periodic
boundaries. But, that should not be a cause for breaking a simulation.
The only parameter you mentioned that could be linked to the stability
of the simulation is the nstcomm, the others only control output.

Of course you should try to understand what made your simulation
crash, in stead of treating symptoms, possibly covering up some flaw
in the set up of the simulation. Check the .log file.


On 3/29/07, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> ? wrote:
> > Hi everybody,
> >
> > I have a problem with my molcule.I have protein- ligand complex.One of
> > my friends works with the same ligand.First of all we use the same mdp
> > files.We made the simulation.But my calculations were halted.This is the
> > error :
> > Error on node 1, will try to stop all the nodes
> > Halting parallel program mdrun_mpi on CPU 1 out of 8
> > 7 additional processes aborted (not shown)
> This is just a generic MPI error message. You haven't established what
> has caused it yet. Try running the system for a short time on a single
> processor, to eliminate parallelism as a source of the problems (you'll
> need to re-grompp, of course).
> >  I only can think about the difference may be caused because of my
> > protein -ligand complex is very big.It has 2 chains.
> >
> > After that I changed
> > nstcomm ,nstxout ,nstvout ,nstfout, nstlog ,nstenergy,  nstxtcout    values
> > than it started to run. But the graphics after the analyze
> > part(rmsd,gyration...) are very bad.I saw very sharp and meaningless
> > pics.
> Probably your topology is broken or your structure is insufficiently
> minimized or equilibrated.
> >Then I would like to do the same thing with a paper.In this paper
> > they made the calculation for 50 ps with position restarint.After they
> > made for 50 ps without position restraint.At the end they made for 20 ns
> > again full mdp.Idid the same.But the gyration and rmsd calculations are
> > not the same.Again meaningless graphics.I have tried to solve the
> > problems for two months.If anything exist to solve the problems I can
> > send my mdp files.Is there a mistake for my mdp files?
> We can't tell yet, since you haven't told us any symptoms that are
> useful diagnostically.
> Mark
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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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