lloyd riggs wrote:
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.
Your system is blowing up. Since it's happening at step 0, it's likely due to
some physically unreasonable geometry. Note that temperature, pressure, etc are
all astronomically high.
Whatever your previous preparation steps (minimization, equilibration), they
were likely insufficient. Otherwise, your .mdp file settings are creating the
problem.
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
-Justin
Hollidays
Stephan Watkins
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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