[gmx-users] confusion about segmentation fault during mdrun

[Lan Hua]

Hi All,

      I understand that the error of segmentation fault may come from many
reasons, but I just couldn't figure out the reason of this error in my
simulations.  I want to run md simulations with explicit water for 20
structures of one domain (residue 77-148) of calmodulin (PDB 1CFC).  These
20 starting structures are from one REMD simulation in implicit water.  The
following is what I did to run simulations for these 20 structures.  I used
gromacs version 3.1.4 with ffamber ports.  The force field is amber03 and
water model is TIP3P.

   1.  get rid of the steric clash in the starting structure
   2.  after doing pdb2gmx, then minimze the protein
   3,   use "-bt dodecahedron -d 0.9 -c"  in the command line of editconf
   4,  after doing genbox, first minimize the water with protein rigid and
then minimize the whole system
   5,  run md simulation with position restraint for protein heavy atoms
with nose-hoover thermostat for 20ps
   6,  run NPT simulations with nose-hoover thermostat and Parrinello-Rahman
thermostat for 500ps
   7,  run NVT simulation for another 100ps
   8, then energy minimze the whole system again.

Every time, there are always "segmentation fault" in step 6 for some
starting structures which could be different in every try.  I checked the
energy, volume, pressure, temperature, etc for the trajectories which are
crashed because of segmentation fault,  but nothing was wrong.  I roughly
checked the trajectory which looks fine.  I also couldn't find any useful
information from the log file, which looks like the following:

           Step           Time         Lambda      Annealing
         180000      360.00003        0.00000        1.00000

   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.045887     47     48   0.004584
        After LINCS         0.000020    752    755   0.000003

   Energies (kJ/mol)
          Angle    Proper Dih. Ryckaert-Bell.          LJ-14     Coulomb-14
    2.08335e+03    1.59908e+02    2.95659e+03    1.17109e+03    1.27711e+04
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coulomb (LR)      Potential
    4.10779e+04   -1.37728e+03   -2.89916e+05   -5.82443e+04   -2.89318e+05
    Kinetic En.   Total Energy    Temperature Pressure (bar)
    5.25584e+04   -2.36759e+05    2.96920e+02   -1.07683e+02

           Step           Time         Lambda      Annealing
         185000      370.00003        0.00000        1.00000

   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.052014     70     71   0.005149
        After LINCS         0.000011    214    215   0.000002

   Energies (kJ/mol)
          Angle    Proper Dih. Ryckaert-Bell.          LJ-14     Coulomb-14
    2.33684e+03    1.42695e+02    2.91169e+03    1.18452e+03    1.28507e+04
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coulomb (LR)      Potential
    4.06987e+04   -1.37332e+03   -2.88889e+05   -5.83180e+04   -2.88455e+05
    Kinetic En.   Total Energy    Temperature

The *.mdp files are also attached.   Any help will be highly appreciated.
Thank you.


Best,
Lan
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