[gmx-users] g_hbond error "Your computational box has shrunk too much"

David van der Spoel spoel at xray.bmc.uu.se
Wed Oct 18 14:21:32 CEST 2006

andrea carotti wrote:
> Hi all,
> I'm beginning to analyze my trajectories, everything works fine with
> (g_rmsf, g_saltbr ...) but when i try to use g_hbond I receive this
> error:
> --------------
> Program g_hbond, VERSION 3.3.1
> Source code file: gmx_hbond.c, line: 631
> Fatal error:
> Your computational box has shrunk too much.
> g_hbond can not handle this situation, sorry.
> -------------------------------------------------------
> Is this a bug or a problme with my system? Is there the possibility to
> avoid this problem in some way?
> Andrea
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Is it correct? Did you plot the box volume as a function of time?
You can use g_hbond for different stretches of the trajectory and 
combine the results manually.
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://folding.bmc.uu.se

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