I missed my Gromacs version. It's 4.0.7 -- Chandan kumar Choudhury NCL, Pune INDIA
On Wed, Apr 13, 2011 at 4:58 PM, Chandan Choudhury <[email protected]>wrote: > 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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