[gmx-users] my big problem

Mark Abraham Mark.Abraham at anu.edu.au
Thu Mar 29 10:18:56 CEST 2007

? 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.


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