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PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

Roe, Daniel R., Cheatham, Thomas E.·2013·Journal of Chemical Theory and Computation
DOI 10.1021/ct400341p
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Abstract

We describe PTRAJ and its successor CPPTRAJ, two complementary, portable, and freely available computer programs for the analysis and processing of time series of three-dimensional atomic positions (i.e., coordinate trajectories) and the data therein derived. Common tools include the ability to manipulate the data to convert among trajectory formats, process groups of trajectories generated with ensemble methods (e.g., replica exchange molecular dynamics), image with periodic boundary conditions, create average structures, strip subsets of the system, and perform calculations such as RMS fitting, measuring distances, B-factors, radii of gyration, radial distribution functions, and time correlations, among other actions and analyses. Both the PTRAJ and CPPTRAJ programs and source code are freely available under the GNU General Public License version 3 and are currently distributed within the AmberTools 12 suite of support programs that make up part of the Amber package of computer programs (see http://ambermd.org ). This overview describes the general design, features, and history of these two programs, as well as algorithmic improvements and new features available in CPPTRAJ.

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Metadata

Authors
Roe, D. R., & Cheatham, T. E.
Venue
Journal of Chemical Theory and Computation
Publisher
American Chemical Society (ACS)
Published
2013-06-25
Volume
9
Issue
7
Pages
3084-3095
ISSN
  • 1549-9618 (ISSN-L)
  • 1549-9626
DOI
10.1021/ct400341p
OpenAlex
W2332712348
Cited by
7,382
References
3
FWCI
53.79
Type
journal article
Language
en
Open access
closed

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