Re: [gmx-users] qm-mm calculation
On 7/14/13 11:36 AM, Nilesh Dhumal wrote: 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 = 500 ; 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 = 5000 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. Debugging code that is nearly 4 years old is not very productive for the development team. If you can reproduce the problem with version 4.6.3, it's more likely to get attention, as countless changes, enhancements, and improvements have taken place in the intervening time, any of which may have implications for whatever it is that you're trying to do. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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] qm-mm calculation
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 = 500 ; 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 = 5000 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 listgmx-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] qm-mm calculation
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 = 500 ; 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 = 5000 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 listgmx-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] QM/MM Calculation with Orca
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 listgmx-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
