Dear GROMACS Users, I am using Gromacs with ORCA for a qm calculation, but I can only use 1 processor for mdrun.
If I place the line !PAL4 in the topol.ORCAINFO and run mdrun -nt 1, it works, and ORCA parallelizes correctly for 4 processors, although mdrun only runs one thread. If I place the line !PAL4 in the topol.ORCAINFO and run mdrun -nt 4, it doesn’t work. mdrun crashes with a segmentation fault error : Back Off! I just backed up md.log to ./#md.log.35# Reading file topol.tpr, VERSION 4.5.5 (single precision) Starting 4 threads QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. there we go! there we go! there we go! there we go! Layer 0 nr of QM atoms 73 QMlevel: B3LYP/STO-3G /opt/soft/orca_2_9_1_linux_x86-64/opt/soft/orca_2_9_1_linux_x86-64... orca initialised... Segmentation fault (core dumped) Is this because mdrun can only run with 1 thread when used with ORCA ? Here’s some information : OS: CentOS 6.2 x86_64 kernel 2.6.32-220 GROMACS: 4.5.5 compiled with options : --with-qmmm-orca --without-qmmm-gaussian ORCA: 2.9.1 for x86_64 OPENMPI: 1.4.3 My minimization mdp file is: ------------ ; ; Input file ; title = Yo ; a string cpp = /lib/cpp ; c-preprocessor integrator = cg ; ;integrator = l-bfgs rlist = 1.0 ; cut-off for ns rvdw = 1.0 ; cut-off for vdw rcoulomb = 1.5 ; cut-off for coulomb ; Energy minimizing stuff ; nsteps = 200 emtol = 10 emstep = 0.1 ;define = -DPOSRES constraints = none QMMM = yes QMMM-grps = MOL QMMMscheme = normal QMbasis = STO-3g QMmethod = b3lyp QMcharge = 1 QMmult = 1 ------------- Thanks in advance -- 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
