scholarly journals PCAViz: An Open-Source Python/JavaScript Toolkit for Visualizing Molecular Dynamics Simulations in the Web Browser

2019 ◽  
Vol 59 (10) ◽  
pp. 4087-4092 ◽  
Author(s):  
Sayuri Pacheco ◽  
Jesse C. Kaminsky ◽  
Iurii K. Kochnev ◽  
Jacob D. Durrant
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Open Source ◽  
Web Browser ◽  
Dynamics Simulations ◽  
The Web

MDBenchmark: A Toolkit to Optimize the Performance of Molecular Dynamics Simulations

2020 ◽  
Author(s):  
Michael Gecht ◽  
Marc Siggel ◽  
Max Linke ◽  
Gerhard Hummer ◽  
Juergen Koefinger
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Open Source ◽  
Material Properties ◽  
Computation Time ◽  
Simulation System ◽  
Software Environment ◽  
Novice Users ◽  
Hardware Configuration ◽  
Dynamics Simulations

Molecular dynamics simulations resolve biomolecular processes and material properties with incomparable detail. As a result, they consume a significant fraction of worldwide supercomputing resources. With our open source benchmarking software MDBenchmark, expert and novice users alike can easily determine the optimal settings for their specific simulation system, MD engine, software environment, and hardware configuration. Ultimately, saving computation time, energy, and money at essentially no additional cost will produce better science.<br>

scholarly journals PBxplore: a tool to analyze local protein structure and deformability with protein Blocks

2017 ◽  
Author(s):  
Jonathan Barnoud ◽  
Hubert Santuz ◽  
Pierrick Craveur ◽  
Agnel Praveen Joseph ◽  
Vincent Jallu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Protein Structure ◽  
Molecular Dynamics Simulations ◽  
Open Source ◽  
Local Structure ◽  
Protein Structures ◽  
Local Protein Structure ◽  
Dynamics Simulations ◽  
Protein Blocks ◽  
Local Protein

ABSTRACTProteins are highly dynamic macromolecules. A classical way to analyze their inner flexibility is to perform molecular dynamics simulations. In this context, we present the advantage to use small structural prototypes, namely the Protein Blocks (PBs). PBs give a good approximation of the local structure of the protein backbone. More importantly, by reducing the conformational complexity of protein structures, they allow analyzes of local protein deformability which cannot be done with other methods and had been used efficiently in different applications. PBxplore is a suite of tools to analyze the dynamics and deformability of protein structures using PBs. It is able to process large amount of data such as those produced by molecular dynamics simulations. It produces various outputs with text and graphics, such as frequencies, entropy and information logo. PBxplore is available at https://github.com/pierrepo/PBxplore and is released under the open-source MIT license.

scholarly journals Practical Implementation of Molecular Dynamics Code for Beginners Using Python

2020 ◽  
Author(s):  
Sumith Yesudasan
Keyword(s):  
Molecular Dynamics ◽  
Graduate Students ◽  
Molecular Dynamics Simulations ◽  
Open Source ◽  
Practical Implementation ◽  
Thermodynamic Quantities ◽  
Input And Output ◽  
Dynamics Simulations

In this paper, we introduce a simple yet powerful and working version of the molecular dynamics code using the Python 3.9 language. The code contents are published in the link given in the appendix 1. The structure and components of the program is given in detail using flowcharts and code snippets. The program consists of major features like velocity verlet integrator, thermostats, COM removal, input and output modules, virial, pressure, and other thermodynamic quantities estimation etc. The author believes that this program will be helpful to graduate students who perform research in molecular dynamics simulations who intend to write their own code instead of the sophisticated open source packages.

scholarly journals PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e4013 ◽  
Author(s):  
Jonathan Barnoud ◽  
Hubert Santuz ◽  
Pierrick Craveur ◽  
Agnel Praveen Joseph ◽  
Vincent Jallu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Protein Structure ◽  
Molecular Dynamics Simulations ◽  
Open Source ◽  
Local Structure ◽  
Protein Structures ◽  
Local Protein Structure ◽  
Dynamics Simulations ◽  
Protein Blocks ◽  
Local Protein

This paper describes the development and application of a suite of tools, called PBxplore, to analyze the dynamics and deformability of protein structures using Protein Blocks (PBs). Proteins are highly dynamic macromolecules, and a classical way to analyze their inherent flexibility is to perform molecular dynamics simulations. The advantage of using small structural prototypes such as PBs is to give a good approximation of the local structure of the protein backbone. More importantly, by reducing the conformational complexity of protein structures, PBs allow analysis of local protein deformability which cannot be done with other methods and had been used efficiently in different applications. PBxplore is able to process large amounts of data such as those produced by molecular dynamics simulations. It produces frequencies, entropy and information logo outputs as text and graphics. PBxplore is available at https://github.com/pierrepo/PBxplore and is released under the open-source MIT license.

MDBenchmark: A Toolkit to Optimize the Performance of Molecular Dynamics Simulations

2020 ◽  
Author(s):  
Michael Gecht ◽  
Marc Siggel ◽  
Max Linke ◽  
Gerhard Hummer ◽  
Juergen Koefinger
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Open Source ◽  
Material Properties ◽  
Computation Time ◽  
Simulation System ◽  
Software Environment ◽  
Novice Users ◽  
Hardware Configuration ◽  
Dynamics Simulations

Molecular dynamics simulations resolve biomolecular processes and material properties with incomparable detail. As a result, they consume a significant fraction of worldwide supercomputing resources. With our open source benchmarking software MDBenchmark, expert and novice users alike can easily determine the optimal settings for their specific simulation system, MD engine, software environment, and hardware configuration. Ultimately, saving computation time, energy, and money at essentially no additional cost will produce better science.<br>

scholarly journals MDBenchmark: A Toolkit to Optimize the Performance of Molecular Dynamics Simulations

2020 ◽  
Author(s):  
Michael Gecht ◽  
Marc Siggel ◽  
Max Linke ◽  
Gerhard Hummer ◽  
Juergen Koefinger
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Open Source ◽  
Material Properties ◽  
Computation Time ◽  
Simulation System ◽  
Software Environment ◽  
Novice Users ◽  
Hardware Configuration ◽  
Dynamics Simulations

Molecular dynamics simulations resolve biomolecular processes and material properties with incomparable detail. As a result, they consume a significant fraction of worldwide supercomputing resources. With our open source benchmarking software MDBenchmark, expert and novice users alike can easily determine the optimal settings for their specific simulation system, MD engine, software environment, and hardware configuration. Ultimately, saving computation time, energy, and money at essentially no additional cost will produce better science.<br>

MDsrv: viewing and sharing molecular dynamics simulations on the web

2017 ◽  
Vol 14 (12) ◽  
pp. 1123-1124 ◽  
Author(s):  
Johanna K S Tiemann ◽  
Ramon Guixà-González ◽  
Peter W Hildebrand ◽  
Alexander S Rose
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations ◽  
The Web
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