[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
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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