[gmx-users] my big problem

özge kül ozgekul8233 at yahoo.com
Thu Mar 29 09:55:39 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)
   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.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?
  thank you ..

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