[gmx-users] memory problems with g_hbond

[Attilio Vargiu]

Many thanks for the suggestion!!!

Attilio

Quoting David <spoel at xray.bmc.uu.se>:

> 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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