Re: average and runningaverage in ptraj

From: Holger Gohlke <>
Date: Wed 06 Nov 2002 08:56:23 -0800


the runningaverage command modifies the state of your trajectory in that
snapshots of a given window length are averaged (and stored internally).
It is this average (instead of the original coordinates), which is then
used in subsequent commands for analyses. For your purpose, the "plain"
average command is the appropriate one.

Best regards


> Could somebody explain me a bit more clear then in the manual what
> exactly is the difference between the average and runningaverage
> commands in ptraj. I am trying to get the average structure from my
> dynamics runs and then minimize it. Which would be a proper way?
> Best regards,
> vlad
> --
> Vlad Cojocaru
> Max Planck Institute for Biophysical Chemistry
> Department: 060
> Am Fassberg 11, 37077 Goettingen, Germany
> tel: ++49-551-201.1389
> e-mail:
> home tel: ++49-551-9963204

Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
Received on Wed Nov 06 2002 - 08:56:23 PST
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