[gmx-users] mdrun no structural output

[reisingere at rostlab.informatik.tu-muenchen.de]

Hi everybody,
I wanted to do a minimization with mdrun but the only output I get is:
3m71_minim.edr
3m71_minim.log
3m71_minim.trr
But no structure file like .pdb i.e.

There was no error in the step before where I prepared the input file with
grompp. My .mdp file looks like this:

define                  = -DPOSRES
integrator              = steep
emtol           = 10
nsteps          = 5000
nstenergy               = 1
energygrps              = System
coulombtype             = PME
rcoulomb                = 0.9
rvdw                    = 0.9
rlist           = 0.9
fourierspacing  = 0.12
pme_order               = 4
ewald_rtol              = 1e-5
pbc                     = xyz



And also in this step there was no error.
The end of the 3m71_minim.log looks like this:

           Step           Time         Lambda
           2647     2647.00000        0.00000

   Energies (kJ/mol)
           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
    5.35530e+02    2.26340e+03    1.17875e+04    1.31106e+02    4.73257e+03
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip. Position Rest.
    6.58188e+04    9.41710e+04   -7.10195e+05   -1.62296e+05    9.89235e+02
      Potential Pressure (bar)
   -6.92062e+05   -3.32594e+03


And the stdout looks like this:

Step= 2646, Dmax= 3.6e-03 nm, Epot= -6.92039e+05 Fmax= 5.12625e+03, atom=
1022
Step= 2647, Dmax= 4.3e-03 nm, Epot= -6.92098e+05 Fmax= 3.72457e+03, atom=
1022
Step= 2647, Dmax= 4.3e-03 nm, Epot= -6.92062e+05 Fmax= 1.51933e+03, atom=
1022
Step= 2648, Dmax= 5.2e-03 nm, Epot= -6.92099e+05 Fmax= 4.25221e+03, atom=
1022
Step= 2648, Dmax= 5.2e-03 nm, Epot= -6.92041e+05 Fmax= 6.45781e+03, atom=
1022

The command for the mdrun was:

mpirun -n 2 $gromacsPath/mdrun_mpi -c $path/3m71_minim.pdb -compact
-deffnm $path/3m71_minim -s $path/3m71_minim_ion.tpr  -v
2>>$path/minLogErr 1>>$path/minLogOut

Can you please tell me whats wrong?

Thank you,
Eva