On Dec 17, 2012, at 9:21 AM, Vijay Manickam Achari <vjrajamany.yahoo.com> wrote:
> Dear Jason,
>
> Actually I already extract the velocity for the water molecules for each frame from trajectory file. But what is missing is the velocity for particular water molecule for all frames. For example, lets say water molecule number 5. What I want is the velocity for that molecule (number 5), starting from frame number 1 until frame number 10000.
> Using python code, it gives only the velocity for all the molecules in a frame but not the appropriate molecular number throughout all frames.
You can actually do the whole calculation in Python using ScientificPython and numpy. The MdoutAnalyzer.py script has code for calculating the normalized autocorrelation function of a data series using numpy.correlate (search for np.correlate).
Also, if you followed the get_restarts.py script, you'll see that the velocities at each frame are stored in a large array, meaning you can access any of the data you want, such as the velocities of the atoms you want specifically.
HTH,
Jason
Ps. In the future please keep these conversations on the mailing list
--
Jason M. Swails
Quantum Theory Project
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Dec 17 2012 - 07:00:03 PST
