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

David van der Spoel spoel at xray.bmc.uu.se
Wed Oct 18 14:57:51 CEST 2006

andrea carotti wrote:
>> 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.
>> -- 
> Thanks for the fast reply.
> I'm only trying to monitor the hbond formation with the " basic" command
> g_hbond -f m93_newtraj.trr -s topol.tpr -n
> and giving to the groups selection two different parts of my protein (i've made an index file)..and then the programs suddenly stop.
> the default output (-num) should be the total number of hbond per frame.
> Please help me again
> Andrea

you haven't answered my question, and haven't read my advice either.

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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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