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trio - TRajectory Input/Output
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Copyright (c) 2000 The Board of Trustees of the University of Illinois
All rights reserved.
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Compiling
---------
Compiling trio is often as simple as running make in the
distribution directory. You may need to modify the Makefile
to set "CC" and "CFLAGS" for your system, set "CC" to the name
of your system's C++ compiler.
Usage
-----
trio [switches] [options] input_file output_file
Description
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Trio converts between molecular dynamics trajectory file formats.
Various options are provided by the commandline switches. The format of
the input file is guessed by its extension, unless it is specified
explicitly on the commandline. The file is then read into memory and
written out to the output file in the format associated with its
filename extension unless explicitly specified.
Trio also allows you to specify a floating-point precision value
(number of digits to be written) for ASCII files, and binary
precision (floats or doubles) for binary files. Binary files also
can be written in an explicit byte ordering for cross-platform
compatibility. Trio automatically detects and corrects for
oppositely-ordered files.
Trio has the following command-line options:
-h Display a commandline help message and exit.
-v Display version information and exit.
-p N Sets floating point precision to N. For ASCII files, this
sets the number of decimal places used when writing floating
point numbers. For binary files, only values of 4 or 8 are
allowed, specifying to use floats or doubles, respectively.
-o FMT Explicitly sets the output file format. See below for a list
of file formats supported by trio.
-i FMT Explicitly sets the input file format.
-r Writes output file using opposite byte-ordering
-s N Skips N frames after every one written. (Specifying a
one here would cause every other step to be skipped.)
-S Skips the first N frames in the input file.
-n N Stops after writing N frames to the output file.
Currently, only four file formats are supported by trio. Its
modular design will allow additional formats to be easily added
in the future. The following are currently supported:
gro - Gromacs coordinates or trajectories (ASCII)
trr - Gromacs trajectory (binary, full precision)
g96 - GROMOS-96 coodinates or trajectory (ASCII)
pdb - Brookhaven Protein Databank coordinates (ASCII)
* dcd - CHARMm/X-PLOR trajectory (binary)
Note: * denotes an input-only format.
Trio also allows structure-only files like gro and pdb to
be made into trajectory files in the conventional manner of
concatenating multiple files, each representing a frame in the
sequence. (g96 files are an exception since their specification
defines that the TITLE block occurs only once when used as a
trajectory file.)
Trio will use this technique to write trajectory data from
files to formats that only contain structure/coordinate data.
Examples
--------
A commandline to simply convert the file trr file 'simul.trr'
to a GROMOS-96 file 'simul.g96':
trio simul.trr simul.g96
To convert the ASCII gro file 'simul.gro' to a binary trr file
'simul.trr' using opposite byte-ordering and full (double)
precision:
trio -r -p 8 simul.gro simul.trr
To delete the first 2 frames and skip every other frame
from a PDB file, and stop after writing 10 frames:
trio -s 1 -S 2 -n 10 simul.pdb newsimul.pdb
Authors
-------
Trio was originally written by David A. Norris, with a little
guidance from John Stone.
Trio is maintained by the Theoretical Biophysics Group at
the Beckman Institute, University of Illinois at Urbana-
Champaign.
Contact
-------
Email: vmd@ks.uiuc.edu Address: 405 N. Mathews Ave.
Urbana, IL 61801 USA
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