[AMBER-Developers] Enhancements and Updates to Cpptraj

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Wed, 14 Nov 2012 10:08:27 -0700

Hello all,

I have recently made some enhancements and updates to cpptraj and
wanted to make you aware of some of them in case you wanted to try
them out.

One of the biggest changes is 'ensemble' reading of trajectories. This
works similar to 'trajin remdtraj' except instead of processing one
frame at a certain temperature, frames at all temperatures are
processed. This means that all action/trajout commands apply to all
members of the ensemble. For example, to read in a replica ensemble,
convert it to temperature trajectories, and calculate a distance at
each temperature:

parm ala2.99sb.mbondi2.parm7
ensemble rem.crd.000 trajnames rem.crd.001,rem.crd.002,rem.crd.003
trajout temp.crd
distance d1 out d1.ensemble.dat .1 @21

This will output 4 temperature trajectories named temp.crd.X, where X
ranges from 0 to 3 with 0 corresponding to the lowest temperature, and
d1.ensemble.dat containing 4 columns, each corresponding to a
temperature. This also means that you can now trajin multiple
ensembles and write single temperature trajectories (which you couldnt
before). The ensemble stuff isnt working for multiD replica yet, thats
coming soon. Small note: trajectory appending is now fixed and working
for all formats.

Another change is the addition of the GNU readline library to improve
interactive mode. This means, among other things, that filename
tab-completion and command history (accessible with the up-arrow) are
now supported. To enter interactive mode just type cpptraj. If you do
not specify an input file or if you specify '--interactive' you will
also enter interactive mode. This can be useful if you want to process
some input from an input file but still want to use the interactive
mode. Note, the ls/head/pwd unix commands are supported from the
cpptraj command line for ease-of-use.

Cpptraj can now read in whitespace delimited data organized in columns
and xmgrace files. This can be useful for reading in previously
generated data to perform analysis.

This is just a quick summary of some of the recent additions; there is
a lot more functionality in there. I've updated the manual for most of
it but it's still a work in progress. Treat the current code as alpha
code - it passes all the current tests but I still have more testing
to do.

If you come across any bugs, have any questions, feedback, or
suggestions please email me.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Nov 14 2012 - 09:30:02 PST
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