[gmx-users] g msd freeze

[Kateřina Hynštová]

>Kateřina Hynštová wrote:
>> Dear users,
>> 
>>  
>> 
>> I would like to calculate the mean square displacement.
>> 
>> Using the
>> 
>>  
>> 
>> g_msd -f traj.xtc -s input.tpr  -n index.ndx -o msd.xvg
>> 
>>  
>> 
>> I get
>> 
>>  
>> 
>> Reading file input.tpr, VERSION 3.3.2(single precision)
>> 
>> Reading file input.tpr, VERSION 3.3.2(single precision)
>> 
>> Group   0(         C) has             1 elements
>> 
>> There is one group in the index
>> 
>> Reading frame 0 time 0.000
>> 
>>  
>> 
>> The system always freezes here without any warning or error. I have 
>
>If your simulation is long and/or computer slow, then it's possible the 
>calculation is still running. If so, you can experiment with the -b, -e, 
>and -dt flags to make the calculation shorter. See g_msd -h. You can 
>also use other analysis tools to check if the problem is localised or not.
The simulated system is a carbon chain of 1000 united atom units. Ive tried bothmaking the system smaller (less units or extracting the trajectory for one unit)and taking very short time of simulation using the flags -b and -e, the system response is still the same (even after the run over weekend) The simulation and all other tools used so far work ok even for much larger systems.Ive also tried the -msd flag in g_analyze tool, I get the msd graph "immediatelly". The system im running the simulation on is currently CPU INTEL Core 2 Quad Q600 (2.4GHz, 8M, 1066MHz), 4x1G DDR2-800 MHz Aeneon BOX. I have also tried to recompile the g_msd tool.Could I be some problem of e.g. memory? I appologize if Im not giving the exact or sufficient informationto about the problem, Im the very begginer. Thank you very much for your help.Best regards,Katka
>Otherwise, how big is the system, how long is the trajectory and what 
>system are you running on?
>
>Mark

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