[gmx-users] my big problem
Mark.Abraham at anu.edu.au
Thu Mar 29 10:18:56 CEST 2007
> 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
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
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