[gmx-users] memory problems with g_hbond

[David]

On Sun, 2005-06-12 at 10:32 +0200, Attilio Vargiu wrote:
> Hi all,
>  I have some problems with memory in analyzing the h-bonds between a 
>  molecule and waters. This is an extract of the output:
>  ------------------------
>  Select a group: 65
>  Selected 65: 'O9_IMI'
>  Select a group: 9
>  Selected 9: 'WAT'
>  Checking for overlap...
>  Calculating hydrogen bonds between two groups of 1 and 24078 atoms
>  Found 0 donors and 1 acceptors in group 'O9_IMI'
>  Found 8026 donors and 8026 acceptors in group 'WAT'
>  Going to allocate 1509953 kb of memory,  and that's only the beginning
>  Killed
>  -------------------------
>  
>  Does someone know how to fix this problem? Is there some possibility 
>  (for example with trjconv) to reduce the size of  the box removing some 
>  water molecule?
You must make an index group where you divide the waters in groups, e.g.
2 groups of half the molecules, then do the analysis on the groups and
combine the results.


>  
>  Thanks in advance, any help will be greatly apprecied!!!!
>  
>  Attilio
>  
>  ---------
>  Attilio Vittorio Vargiu
>  Ph.D. Student at SISSA/ISAS, via Beirut 4 34014 Trieste, Italy
>  Phone: +39-040-3787335, Fax  : +39-040-3787528
>  
> 
> 
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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