[gmx-users] fatal error

lmao lmao at rufus.biomed.brown.edu
Sat Oct 29 02:58:27 CEST 2005


I am using Gromacs-3.3 to test a simply setup with 1 aa (Arg) soaked into decane and h2o box. I built decane in opls force field and equalibrate in 500 ps. I got the  following errow message:
Going to use C-settle (3503 waters)
wo = 0.888096, wh =0.0559521, wohh = 18.0154, rc = 0.08165, ra = 0.00646074
rb = 0.0512738, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1

Constraining the coordinates at t0-dt (step -1)
Started mdrun on node 0 Fri Oct 28 20:32:25 2005
Initial temperature: 1.5005e-06 K
           Step           Time         Lambda
              0        0.00000        0.00000

Grid: 10 x 10 x 10 cells
Configuring nonbonded kernels...
Testing x86_64 SSE support... present.

There are 27 atoms in your xtc output selection
   Energies (kJ/mol)
           Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
    1.01299e+04    1.46256e+04    2.51058e-02    5.28688e+03    3.10635e+03
     Coulomb-14        LJ (SR)        LJ (LR)   Coulomb (SR)   Coulomb (LR)
   -1.47135e+03    5.50145e+04   -5.19759e+02   -1.55182e+05    9.38746e+02
      Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
   -6.80710e+04    5.46591e+04   -1.34119e+04    2.94057e+02    1.36892e+04

Step 3  Warning: pressure scaling more than 1%, mu: 4.91917e+09 4.91917e+09 4.91917e+09

Step 4  Warning: pressure scaling more than 1%, mu: 4.57705e+09 4.57705e+09 4.57705e+09

t = 0.004 ps: Water molecule starting at atom 18406 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates
Grid: -2147483648 x -2147483648 x -2147483648 cells
Program mdrun, VERSION 3.3
Source code file: nsgrid.c, line: 220

Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.

I noticed Berk found one bug in nsgrid.c file before in 3.3-beta version when it is running on SGI. But I am using 64-bit Linux w/ 3.3 version and the bug should be fixed. Does anyone what the problem is? Thanks.


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