Hello, I am trying to run the qm-mm gas phase calculations for my system. I am using following in md.mdp file.
title = cpeptide MD cpp = /usr/bin/cpp integrator = md dt = 0.001 ; ps ! nsteps = 5000000 ; total 5 ps. nstcomm = 1 nstxout = 1 nstvout = 1 nstfout = 1 nstlist = 1 ns_type = simple rlist = 0.0 rcoulomb = 0.0 rvdw = 0.0 coulombtype = cut-off vdwtype = cut-off pbc = no fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on Tcoupl = nose-hoover tau_t = 0.1 tc-grps =system ref_t = 350 ; Pressure coupling is on Pcoupl = no ;Parrinello-Rahman pcoupltype = isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 350.0 gen_seed = 173529 QMMM = yes QMMM-grps = System QMmethod = RHF QMbasis = 3-21G QMcharge = 0 QMmult = 1 I could run the grompp and for mdrun I am getting following error. Back Off! I just backed up md.log to ./#md.log.2# Reading file 1.tpr, VERSION 4.0.7 (single precision) QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 32 QMlevel: RHF/3-21G number of CPUs for gaussian = 1 memory for gaussian = 50000000 accuracy in l510 = 8 NOT using cp-mcscf in l1003 Level of SA at start = 0 [c63:25888] *** Process received signal *** [c63:25888] Signal: Segmentation fault (11) [c63:25888] Signal code: Address not mapped (1) [c63:25888] Failing at address: (nil) [c63:25888] [ 0] /lib64/libpthread.so.0 [0x2b2d89ac1a90] [c63:25888] [ 1] /lib64/libc.so.6(strlen+0x40) [0x2b2d89d4b590] [c63:25888] [ 2] /lib64/libc.so.6(fputs+0x1e) [0x2b2d89d33dde] [c63:25888] [ 3] mdrun(init_gaussian+0x4c3) [0x51e993] [c63:25888] [ 4] mdrun(init_QMMMrec+0xef8) [0x517578] [c63:25888] [ 5] mdrun(mdrunner+0x1019) [0x42e109] [c63:25888] [ 6] mdrun(main+0x3c5) [0x434b95] [c63:25888] [ 7] /lib64/libc.so.6(__libc_start_main+0xe6) [0x2b2d89ced586] [c63:25888] [ 8] mdrun [0x415cb9] [c63:25888] *** End of error message *** Segmentation fault Could you tell what is the problem. Nilesh -- 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