Re: average and runningaverage in ptraj

From: Thomas Cheatham <>
Date: Wed 6 Nov 2002 09:36:56 -0800 (PST)

> 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?

The "average" command is what you are looking for; this will take a whole
series of snapshots and then produce a single structure that is a straight
coordinate average. The syntax is as follows:

  average filename [mask] [start start#] [stop stop#] \
   [offset offset#] [pdb [parse | dumpq] | binpos | rest] [nobox] [stddev]

You must give an output filename (filename) immediately after the average
keyword. This file will be an AMBER restart by default. You can instead
output a pdb or binpos file by specification of the keyword. The "parse"
or "dumpq" keywords, when specified with the pdb keyword, will dump
charges and parse radii (parse) or charges and vdw radii (dumpq) into the
temperature/occupancy columns of the pdb file. The "nobox" keyword is
only really useful with the "rest" restart file format. If instead of the
average coordinates, you want to dump the standard deviations, specify the
"stddev" keyword.

If you do not want to dump averages of all the coordinates, specify a
mask. If you do not want all the frames, you can subselect on those
chosen with the the start/stop/offset keywords.

Running average, on the other hand, is useful for smoothing an entire
trajectory; it allows you to create a new trajectory where each frame in
the trajectory is an average over the specified number of frames; if you
did a running average over more frames than are present in the trajectory,
this would be equivalent to the average command and if you did a running
average over 1 frame, you would not alter the trajectory. A value in the
range of 5-25 provides decent smoothing of the high frequency motions and
may be useful for movie generation, etc.

Let me know if you have further questions,

\ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
| Departments of Medicinal Chemistry and of University of Utah
| Pharmaceutics and Pharmaceutical Chemistry 30 South 2000 East, Room 201
| & Center for High Performance Computing Salt Lake City, Utah 84112
| e-mail: phone: (801) 587-9652 FAX: (801) 585-9119
\ Offices: BPRP295A / INSCC 418
Received on Wed Nov 06 2002 - 09:36:56 PST
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