[gmx-users] fatal error
lmao
lmao at rufus.biomed.brown.edu
Sat Oct 29 19:56:55 CEST 2005
Hi David,
Thanks for your reply. My both decane and water box were equilibrated and whole system including Arg, decane and water were minimized before MD run. When I turned off pressure coupling, I got the following error:
__________________
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
Large VCM(group rest): -0.00728, -0.00014, -0.00028, ekin-cm: 2.60597e+00
t = 0.004 ps: Water molecule starting at atom 10492 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates
Large VCM(group rest): 0.02091, 0.00872, 0.00792, ekin-cm: 2.83125e+01
t = 0.006 ps: Water molecule starting at atom 10492 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates
t = 0.008 ps: Water molecule starting at atom 15730 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates
Large VCM(group rest): -0.01551, 0.00200, 0.00038, ekin-cm: 1.20326e+01
t = 0.009 ps: Water molecule starting at atom 17551 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates
Large VCM(group rest): 0.16591, -0.15937, 0.03273, ekin-cm: 2.65363e+03
t = 0.010 ps: Water molecule starting at atom 17953 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates
-------------------------------------------------------
Program mdrun, 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 -2147483648. It should have been within [ 0 .. 1000 ]
Please report this to the mailing list (gmx-users at gromacs.org)
-------------------------------------------------------
____________________________
And also when I used Gromace-3.2.1 on another Linux(32-bit) to run the same job, I got the following error written in a huge file untill my HD is full :
______________________
Testing x86 processor CPUID...
CPU manufactured by Intel.
Testing x86 SSE capabilities...
CPU and OS support SSE.
Using Gromacs SSE single precision assembly innerloops.
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 2.51046e-02 5.28688e+03 3.10496e+03
Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR)
-1.47099e+03 5.50134e+04 -5.19757e+02 -1.55136e+05 9.38096e+02
Potential Kinetic En. Total Energy Temperature Pressure (bar)
-6.80276e+04 1.74910e+04 -5.05365e+04 9.40990e+01 1.46095e+04
Step 3 Warning: pressure scaling more than 1%, mu: 42550.7 42550.7 42550.7
t = 0.003 ps: Water molecule starting at atom 15844 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates
Step 4 Warning: pressure scaling more than 1%, mu: 75083.8 75083.8 75083.8
t = 0.004 ps: Water molecule starting at atom 18400 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates
Large VCM(group rest): 0.17206, 0.12119, 0.12436, ekin-cm: 2.93671e+03
Step 5 Warning: pressure scaling more than 1%, mu: -1.94523 -1.94523 -1.94523
t = 0.005 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
Correcting invalid box:
old box (3x3):
old box[ 0]={-3.73024e+10, 0.00000e+00, -0.00000e+00}
old box[ 1]={ 0.00000e+00, -3.73024e+10, -0.00000e+00} old box[ 2]={ 0.00000e+00, 0.00000e+00, -3.73024e+10}
new box (3x3):
new box[ 0]={-3.73024e+10, 0.00000e+00, -0.00000e+00}
new box[ 1]={ 0.00000e+00, -3.73024e+10, -0.00000e+00}
new box[ 2]={ 0.00000e+00, 3.73024e+10, -3.73024e+10}
Correcting invalid box:
old box (3x3):
old box[ 0]={-3.73024e+10, 0.00000e+00, -0.00000e+00}
old box[ 1]={ 0.00000e+00, -3.73024e+10, -0.00000e+00}
old box[ 2]={ 0.00000e+00, 3.73024e+10, -3.73024e+10}
new box (3x3):
new box[ 0]={-3.73024e+10, 0.00000e+00, -0.00000e+00}
new box[ 1]={ 0.00000e+00, -3.73024e+10, -0.00000e+00}
new box[ 2]={ 0.00000e+00, 7.46048e+10, -3.73024e+10}
_____________________________
My previous test with decane(non-opls ff) worked fine. The only change I made for current test is to build decane in opls ff instead. No clue so far! Thanks for any help!
Best,
lmao
>
> 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
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
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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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