> > > On 6/12/12 5:54 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> Hi everybody, >> I tried to run a minimization just of the hydrogen of a membrane >> protein. >> I want to do this in vacuum. >> >> But when I started the run with >> >> mpirun mdrun_mpi -deffnm protein -v -nt 2 >> >> I get the error that there is a segmentation fault. > > Threading and MPI parallelization are independent. You can't use both. > If > you've compiled with MPI support, you can't invoke the -nt option.
okey, I'll try it without the -nt option. But I still get the error > >> But when I only type >> >> mpirun mdrun_mpi >> >> there is no problem so I guess that my already produced input files are >> the problem. For example I am not completely sure about the .mdp file. >> Can >> you please give me an example for a .mdp file for a minimization of only >> the hydrogen but not the whole protein in a vacuum. >> > > It would be far more useful for you to post what you're using so we can > provide The .mpd file I use looks like this: define = -DPOSRES integrator = md tinit = 0 dt = 0.005 nsteps = 20000 nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 1000 nstxtcout = 1000 nstenergy = 1000 energygrps = Protein Non-Protein nstcalcenergy = 5 nstlist = 5 ns-type = Grid pbc = xyz rlist = 0.9 coulombtype = Cut-off rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 298 298 Pcoupltype = Isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = no constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = yes lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 implicit_solvent = GBSA gb_algorithm = HCT nstgbradii = 1.0 rgbradii = 0.9 gb_epsilon_solvent = 80 gb_dielectric_offset = 0.009 sa_algorithm = Ace-approximation > feedback. The fact that the second command works while the first fails > should > lead to the opposite conclusion - your input is fine, but your invocation > of > mdrun was incorrect. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > -- > 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 > -- 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