Hello gmx-users !! I tried using g_hbond tool to analyse h-bonds on my system. I could successfully execute the tool for two of my systems. But the third system should the memory problem. Below I have pasted my command and its output.
*$ g_hbond -s ../md0-20.tpr -f 40-50.trr -n index_2.ndx -num hbnum.xvg -dist hbdist.xvg -ang hbang.xvg -life hblife.xvg -nice 0 -xvgr No option -sel Reading file ../md0-20.tpr, VERSION 4.0.7 (single precision) Specify 2 groups to analyze: Group 0 ( System) has 95687 elements Group 1 ( HNP) has 10 elements Group 2 ( PE) has 192 elements Group 3 ( HP) has 216 elements Group 4 ( CPE) has 9 elements Group 5 ( SOL) has 95235 elements Group 6 ( Cl) has 25 elements Group 7 ( N_H) has 126 elements Select a group: 5 Selected 5: 'SOL' Select a group: 7 Selected 7: 'N_H' Checking for overlap in atoms between SOL and N_H Calculating hydrogen bonds between SOL (95235 atoms) and N_H (126 atoms) Found 31795 donors and 31795 acceptors ------------------------------------------------------- Program g_hbond, VERSION 4.0.7 Source code file: smalloc.c, line: 147 Fatal error: Not enough memory. Failed to calloc 31795 elements of size 4 for hb->hbmap[i] (called from file gmx_hbond.c, line 186) ------------------------------------------------------- "I Solve Problems" (Pulp Fiction) : Cannot allocate memory Making hbmap structure...* Kindly help. -- Chandan kumar Choudhury NCL, Pune INDIA
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