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

Omer Markovitch omermar at gmail.com
Wed Nov 26 09:49:14 CET 2008

On Tue, Nov 25, 2008 at 01:47, Suman Chakrabarty
<suman at sscu.iisc.ernet.in>wrote:

> 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? Or I need to combine all
> files into a single one anyway?

You should analyze each individual part on its own, and output the raw data
of the result, then average the parts together.

For example - say you are interested in coordination number of molecule X:
For each part, output both the total number of X's found, plus the total
number of X neighbors found. The coordination number is then the sum of
neig. divided by the sum of X's, from ALL parts.
It might be an issue if each part has different time length, then averaging
the coordination number of each part might give more statistical weigh to
short parts then they should have.

In other words, you should first collect the data of each part together, and
only then avg..

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