[gmx-users] g_dist problems

Edvin Erdtman edvin.erdtman at nat.oru.se
Tue May 22 16:31:59 CEST 2007

David van der Spoel skrev:
> 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
>> 216.5000
>>>> 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?
I'm running on a Mandriva 2006 machine, installed with the rpm for 
GROMACS VERSION 3.3.1 (single precision)
> How big is the trajectory file?
103Mb, for this (an 1ns run). Others may be up to 2Gb.
> Does it really stop, or did you not wait long enough? (counter output 
> is logarithmic)
Yes, I'm waiting long enough I guess. I always stops at the same spot in 
that trajectory. I tried to start it later, and then sometimes it gets a 
little bit longer, but then it stops quite soon again. Another similar 
trajectory doesn't stop at all, and another stops at  122.0000076 instead.
Some just stops at :
Reading frame       0 time    0.000  
with zero output


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