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