[gmx-users] Re: g_hbond error

[Erik Marklund]

Certain options require an amount of memory that is proportional to na x 
nd x t, where na and nd are number of acceptors and donors, and t is 
time. You need more memory. Or you could do your calculation for a 
subset of your solvent.

Erik

Chandan Choudhury skrev 2011-04-13 13.29:
> 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 
> <mailto: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
>
>


-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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