[gmx-users] Re:Crash error

[lloyd riggs]

Dear All,

I had posted part of the error below.  I still have not the problem solved, everything from gromacs runs, including short energy minimizations, but if I run an MD I get the log ending;

Started mdrun on node 0 Thu Dec  9 16:56:10 2010

           Step           Time         Lambda
              0        0.00000        0.00000

Grid: 10 x 10 x 10 cells
Long Range LJ corr.: <C6> 2.3566e-03
Long Range LJ corr.: Epot    -59.767, Pres:  -0.198483, Vir:    29.8835
   Energies (kJ/mol)
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
    1.19873e+04    5.04804e+03    5.15110e+03    1.67253e+03    1.49605e+00
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.
    1.15200e+05    2.87676e+09   -5.97670e+01   -1.24355e+05   -7.20279e+04
      Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
    2.87670e+09    4.35260e+17    4.35260e+17    4.13944e+15    9.63648e+14

________________________

and the error log;


Reading file /home/ubelix/l_insel_ria/l_watkins/gormacswork/Test4gromacs/md1.tpr, VERSION 4.0.7 (double precision)
starting mdrun 'Protein'
100000 steps,    200.0 ps.
[cnode33:13647] *** Process received signal ***
[cnode33:13647] Signal: Segmentation fault (11)
[cnode33:13647] Signal code: Address not mapped (1)
[cnode33:13647] Failing at address: 0x237fa90
[cnode33:13647] [ 0] /lib/libpthread.so.0(+0xf010) [0x2b6e69c97010]
[cnode33:13647] [ 1] /usr/lib/libgmx_mpi_d.so.5(+0x115564) [0x2b6e69491564]
[cnode33:13647] *** End of error message ***

I am trying still to find out how to fix it, and if it is a problem with the two files listed, or they are just the last ones called.

Hollidays

Stephan Watkins
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