[gmx-users] fatal error
David
spoel at xray.bmc.uu.se
Sat Oct 29 20:45:22 CEST 2005
On Sat, 2005-10-29 at 13:56 -0400, lmao wrote:
> 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:
Your starting structure is still not good, as you can see from LJ energy
and pressure. Check it in e.g. pymol.
> __________________
> 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
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > --
> > 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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> >
>
> _______________________________________________
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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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