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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists