[gmx-users] System exploided befor runing

Florian Dommert dommert at fias.uni-frankfurt.de
Mon Sep 15 09:53:53 CEST 2008

* Morteza Khabiri <khabiri at greentech.cz> [2008-09-15 01:14:56 +0200]:

>I have a following problem. Last time I send it to gromacs user but I
>couldn't get proper reply.
>I make the solution box of organic solvent. It is homeogen and mixed
>It also has a minimum energy. I put one protein in this solution. Before
>put the protein in the solution I minimimized it also. Now I mixed 2
>system which each of them are minimized. After put the protein in the
>solution I try first to minimized it then run it but unfortunately it
>crashed. It did not work at all. I also tried to run the system without
>minimization but it also did not work at all. I try with opls forcefield
>also (I guess maybe the proble is from forcefield) but it also did not
>work. After runing befor starting to run or minimization (no difference) I
>faced with following message:
>Range checking error:
>Explanation: During neighborsearching, we assign each particle to a grid
>based on its coordinates. If your system contains collisions or parameter
>errors that give particles very high velocities you might end up with some
>coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
>put these on a grid, so this is usually where we detect those errors.
>Make sure your system is properly energy-minimized and that the potential
>energy seems reasonable before trying again.


  as it seems some of the atoms "overlap" meaning their interaction
  forces going to infinity as mentioned in the gromacs warning. This
  might probably occur at the PBC of your box. Since I am not dealing
  with proteins, i do not know the procedure to mix protein and solvent.
  Perhaps the problem is the insertion of the protein in the solvent box.
  If you do it the other way round, putting solvent in an empty box with
  a protein might circumvent the occuring porblem, since it is much more
  easier to fit small molecules into free space than a verly large one.
  Another suggestion for the first test is tho enlarge your box a little
  bit, that you have no overlaps at the boundaries.
  Best Regards

>Variable ci has value -2147483648. It should have been within [ 0 .. 5832 ]
>Please report this to the mailing list (gmx-users at gromacs.org)
>As i mention I could not EM my system. The above event occurs before EM
>and MD running.
>Thats very nice of you if you guid me what should i do?
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Florian Dommert

Computational and Theoretical Softmatter & Biophysics group

Frankfurt Institute for Advanced Studies
Johann-Wolfgang-Goethe University

Ruth-Moufang-Str. 1
60438 Frankfurt am Main

Phone: +49(0)69 / 798 - 47522
Fax:   +49(0)69 / 798 - 47611

EMail: dommert at fias.uni-frankfurt.de
Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert
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