I'm trying to analyzing hydrogen bonds between a DNA and protein complex. When using the -ac option of gmx hbond, I'm getting segmentation faults which look like an out-of-memory problem.
However, I'm giving the process 64gb of memory, and an additional 64gb of virtual memory. How memory intenstive is this program?? Note I am using version 5.1.13. A snippet of the output is below Calculating hydrogen bonds between DNA_interface (919 atoms) and Protein_interface (1026 atoms) Found 138 donors and 458 acceptors Making hbmap structure...done. ... Found 117 different hydrogen bonds in trajectory Found 156 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped - Reduced number of hbonds from 117 to 116 - Reduced number of distances from 156 to 156 Average number of hbonds per timeframe 16.544 out of 31602 possible ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media J. Phys. Chem. B 110 (2006) pp. 4393-4398 -------- -------- --- Thank You --- -------- -------- Doing autocorrelation according to the theory of Luzar and Chandler. [hpc3338:34436] *** Process received signal *** [hpc3338:34436] Signal: Segmentation fault (11) [hpc3338:34436] Signal code: Address not mapped (1) [hpc3338:34436] Failing at address: 0xfde7c370 [hpc3338:34436] [ 0] /lib64/libpthread.so.0(+0xf370)[0x7ff5c3810370] [hpc3338:34436] [ 1] /usr/usc/gromacs/5.1.3/cpu/lib64/libgromacs_mpi.so.1(+0x464449)[0x7ff5c4a7b449] [hpc3338:34436] [ 2] /usr/usc/gromacs/5.1.3/cpu/lib64/libgromacs_mpi.so.1(cross_corr+0x39)[0x7ff5c4a7b019] [hpc3338:34436] [ 3] /usr/usc/gromacs/5.1.3/cpu/lib64/libgromacs_mpi.so.1(+0x339bb2)[0x7ff5c4950bb2] [hpc3338:34436] [ 4] /usr/usc/gromacs/5.1.3/cpu/lib64/libgromacs_mpi.so.1(gmx_hbond+0x312e)[0x7ff5c4947aae] [hpc3338:34436] [ 5] /usr/usc/gromacs/5.1.3/cpu/lib64/libgromacs_mpi.so.1(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x267)[0x7ff5c47b4637] [hpc3338:34436] [ 6] gmx_mpi(main+0xba)[0x40bfea] [hpc3338:34436] [ 7] /lib64/libc.so.6(__libc_start_main+0xf5)[0x7ff5c2c01b35] [hpc3338:34436] [ 8] gmx_mpi[0x40be69] [hpc3338:34436] *** End of error message *** Am I doing something wrong here? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.