[gmx-users] version 3.3 - Range checking error

Joanne Hanna J.F.Hanna at warwick.ac.uk
Fri Nov 25 10:35:34 CET 2005


I have recently tried to re run a simualtion with gromacs v3.3 in double precision that I have managed to run in v3.2.1 single prescision and v3.3 single precision. This simulations is failing with the following error:


           Step           Time         Lambda
         104000      208.00000        0.00000

   Energies (kJ/mol)
       G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
    8.43377e+03    3.79108e+03    2.53005e+03    3.13091e+02    5.79138e+04
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
    1.38869e+05   -1.05323e+06   -1.68330e+05   -1.00971e+06    1.91922e+05
   Total Energy    Temperature Pressure (bar)
   -8.17790e+05    3.11754e+02    4.49698e+01

Program mdrun_d, VERSION 3.3
Source code file: nsgrid.c, line: 226

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 5926. It should have been within [ 0 .. 5760 ]
Please report this to the mailing list (gmx-users at gromacs.org)

"Clickety Clickety Click" (System Manager From Hell)


Could anyone please explain to me what I have done wrong? Should I have re-do the entire process with the double preision? i.e. from starting structure, solvate minimise, md with posres on protein to equilib water and then run my simualtion?

Many thanks

Joanne Hanna
Department of Chemistry
University of Warwick

J.F.Hanna at warwick.ac.uk

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