[gmx-users] g_dist problems
David van der Spoel
spoel at xray.bmc.uu.se
Tue May 22 16:14:19 CEST 2007
Edvin Erdtman wrote:
> Hi again...
>> How can we tell? You haven't given us your command line, or a
>> meaningful chunk of output.
> my command:
> g_dist -f traj.xtc -n index.ndx -s topol.tpr
> The output:
> Select a group: 0
> Selected 0: 'DPPC'
> Select a group: 1
> Selected 1: 'AL'
> Reading frame 0 time 0.000 Back Off! I just backed up dist.xvg
> to ./#dist.xvg.1#
> Reading frame 400 time 200.000
> -and then it stops! I need to hit ctrl-c
> dist.xvg ends:
> 216.0000153 3.7260792 2.1281288 1.1397107 -2.8382730
>>> I tried to convert the trajectory using trjconv -pbc, but non of the
>>> options seems to work.
> I thought that it maybe would help. Someone else (who had send a message
> to this list Bug ? in PBC in g_dist, July 2006) had some problems with
> g_dist and tried to convert the trajectory.
Which compiler did you use?
How big is the trajectory file?
Does it really stop, or did you not wait long enough? (counter output is
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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