Journal ArticleDOI
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
Daniel R. Roe,Thomas E. Cheatham +1 more
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TLDR
PTRAJ and its successor CPPTRAJ are described, two complementary, portable, and freely available computer programs for the analysis and processing of time series of three-dimensional atomic positions and the data therein derived.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://ambe...read more
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Journal ArticleDOI
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
James Maier,Carmenza Martinez,Koushik Kasavajhala,Lauren Wickstrom,Kevin Hauser,Carlos Simmerling +5 more
TL;DR: Together, these backbone and side chain modifications (hereafter called ff14SB) not only better reproduced their benchmarks, but also improved secondary structure content in small peptides and reproduction of NMR χ1 scalar coupling measurements for proteins in solution.
Journal ArticleDOI
PLUMED 2: New feathers for an old bird
TL;DR: This work presents PLUMED 2 here—a complete rewrite of the code in an object-oriented programming language (C++), which introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs.
Journal ArticleDOI
MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories
Robert T. McGibbon,Kyle A. Beauchamp,Matthew P. Harrigan,Christoph Klein,Jason M. Swails,Carlos X. Hernández,Christian R. Schwantes,Lee-Ping Wang,Thomas J. Lane,Vijay S. Pande +9 more
TL;DR: MDTraj is a modern, lightweight, and fast software package for analyzing MD simulations that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python.
Journal ArticleDOI
Lipid14: The Amber Lipid Force Field
Callum J. Dickson,Benjamin D. Madej,Åge A. Skjevik,Robin M. Betz,Knut Teigen,Ian R. Gould,Ross C. Walker +6 more
TL;DR: The AMBER lipid force field has been updated to create Lipid14, allowing tensionless simulation of a number of lipid types with the AMBER MD package, and is compatible with theAMBER protein, nucleic acid, carbohydrate, and small molecule force fields.
Journal ArticleDOI
Molecular Dynamics Simulation for All.
TL;DR: The types of information molecular dynamics simulations can provide and the ways in which they typically motivate further experimental work are described.
References
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MPI-2: Extending the Message-Passing Interface
Al Geist,William Gropp,Steven Huss-Lederman,Andrew Lumsdaine,Ewing Lusk,William Saphir,Tony Skjellum,Marc Snir +7 more
TL;DR: The salient aspects of the evolving MPI-2 document as it now stands are presented and proposed extensions and enhancements to MPI in the areas of dynamic process management, one-sided operations, collective operations, new language binding, real-time computing, external interfaces, and miscellaneous topics are discussed.
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Journal ArticleDOI
Insights into the mobility of methyl-bearing side chains in proteins from 3JCC and 3JCN couplings
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Journal ArticleDOI
Evaluation of DOCK 6 as a pose generation and database enrichment tool
Scott R. Brozell,Sudipto Mukherjee,Trent E. Balius,Daniel R. Roe,David A. Case,Robert C. Rizzo +5 more
TL;DR: Overall, the breadth and number of experiments performed provide a useful snapshot of current capabilities of DOCK6 as well as starting points to guide future development efforts to further improve sampling and scoring.