Hi everybody, I want to do a md run for my membrane protein. For this I first did the energy minimization run. This finished with no errors. Here is the output of it:
Steepest Descents did not converge to Fmax < 10 in 5001 steps. Potential Energy = -8.7463000e+05 Maximum force = 4.5984982e+02 on atom 1107 Norm of force = 5.0847759e+00 The mdp file contains: 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 Now I want to do a NVT to run to prepare the MD run. But here I get the error: Segmentation fault mdrun -nice 0 -c protein.pdb -compact -deffnm protein -s protein.tpr -v 2>> nvtLogErr >> nvtLogOut And there are is no protein.pdb file as output but only step.pdb files like step43b_n6.pdb The mdp file looks like this: define = -DPOSRES integrator = md dt = 0.005 nsteps = 10000 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 0 nstenergy = 5 energygrps = Protein Non-Protein nstcalcenergy = 5 nstlist = 10 ns-type = Grid pbc = xyz rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 gen_vel = yes gen_temp = 200.0 gen_seed = 9999 constraints = all-bonds tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 298 298 pcoupl = no I already did this but the last time I fixed all atoms except of the hydrogen atoms because I wanted to do a MD run with them and keep the rest of the structure. But know I want to do the MD run with all the side chains. And now the error occurs. Can you please tell me what a segmentation fault means? Is this because of the mdp file or because of the protein? Thank you, Eva -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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
