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Hi all, Very recently, I meet a problem when using g_hbond (gromacs 4.5.3 with the bugfixed) ********************************* Select a group: Selected 1: 'SOL' Select a group: Selected 1: 'SOL' Calculating hydrogen bonds in SOL (98280 atoms) Found 32760 donors and 32760 acceptors Segmentation fault ********************************* I check the code of gmx_hbond.c. The problem comes from the function of "mk_hbmap". However, g_hbond doesn't complain "gmx_fatal(FARGS,"Could not allocate enough memory for hbmap")' while giving the "Segmentation fault". My first guess is 1) the function doesn't work correctly; 2) there is no enough memory for 32760 donors and 32760 acceptors. What I really want to calculate is the HB correlation function is some slab structure of thickness of about 3ns, where there is only ~3000 waters. Can someone give me some suggestions? Thanks a lot! best regards, Baofu Qiao |
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