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
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