[gmx-users] System exploided befor runing

Morteza Khabiri khabiri at greentech.cz
Mon Sep 15 01:14:56 CEST 2008


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.

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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