[gmx-users] System exploided befor runing

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 15 03:12:14 CEST 2008

Morteza Khabiri wrote:
> Dear
> I have a following problem. Last time I send it to gromacs user but I
> couldn't get proper reply.

Can you be more specific about what was not "proper" about the advice I gave you 


If you are asking for free help, it is best to demonstrate you have made some 
effort to follow the advice you've been given, especially if you're posting a 
duplicate question, which usually usually get ignored.

Also search the list archive for the error message you have shown below.  There 
are nearly 200 posts related to that specific error.


> I make the solution box of organic solvent. It is homeogen and mixed
> properly.
> 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.
> 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?
> Thanks
> Morteza
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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