[gmx-users] Re: g_hbond error

[Chandan Choudhury]

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 <iitdckc at gmail.com>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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110413/d8dd5075/attachment.html>