[gmx-users] Analyzing a trajectory split over multiple files

Nicolas nsapay at ucalgary.ca
Tue Nov 25 01:53:44 CET 2008

Suman Chakrabarty a écrit :
> Dear all,
> I have a very long trajectory split over a large number of files. What
> would be the most efficient way to use the analysis programs over them?
> Do they support multiple input for trajectory? 
No most of the time, but you can easily analyze each part of your 
trajectory by embedding the Gromacs command line in a while loop. In 
Bash, it gives something like:

    while [ $i -le $npart ]; do
        g_xxx ... >& g_xxx.out

> Or I need to combine all
> files into a single one anyway?
I guess it depends on the time scale of the phenomenon you want to 
observe and on how often you have sample your 
coordinates/velocity/energy during the computation. For a short time 
scale phenomenon, like bond stretching, you can split your trajectory 
into pieces of, let say, 5 ns and consider each piece as independent. 
For a long time scale phenomenon, you will have to split your trajecory 
in bigger pieces or even merge all the parts.
> Please help.
> Regards,
> Suman.

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