[gmx-users] fatal error

[David]

On Fri, 2005-10-28 at 20:58 -0400, lmao wrote:
> Hi,
> 
> 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

You have very high LJ (SR) and pressure. Did you minimize properly after
inserting the Arg? If yes, try running without pressure coupling first.

> 
> 
> 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.
> 
> lmao 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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