[gmx-users] g_hbond error

Chandan Choudhury iitdckc at gmail.com
Wed Apr 13 13:28:52 CEST 2011

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
(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
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