TRAVIS—A free analyzer for trajectories from molecular simulation
TRAVIS (“Trajectory Analyzer and Visualizer”) is a program package for post-processing and analyzing trajectories from molecular dynamics and Monte Carlo simulations, mostly focused on molecular condensed phase systems. It is an open source free software licensed under the GNU GPL, is platform indep...
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| Published in | The Journal of chemical physics Vol. 152; no. 16; pp. 164105 - 164124 |
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| Main Authors | , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
American Institute of Physics
30.04.2020
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| Subjects | |
| Online Access | Get full text |
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| Abstract | TRAVIS (“Trajectory Analyzer and Visualizer”) is a program package for post-processing and analyzing trajectories from molecular dynamics and Monte Carlo simulations, mostly focused on molecular condensed phase systems. It is an open source free software licensed under the GNU GPL, is platform independent, and does not require any external libraries. Nine years after the original publication of TRAVIS, we highlight some of the recent new functions and features in this article. At the same time, we shortly present some of the underlying algorithms in TRAVIS, which contribute to make trajectory analysis more efficient. Some modern visualization techniques such as Sankey diagrams are also demonstrated. Many analysis functions are implemented, covering structural analyses, dynamical analyses, and functions for predicting vibrational spectra from molecular dynamics simulations. While some of the analyses are known since several decades, others are very recent. For example, TRAVIS has been used to compute the first ab initio predictions in the literature of bulk phase vibrational circular dichroism spectra, bulk phase Raman optical activity spectra, and bulk phase resonance Raman spectra within the last few years. |
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| AbstractList | TRAVIS ("Trajectory Analyzer and Visualizer") is a program package for post-processing and analyzing trajectories from molecular dynamics and Monte Carlo simulations, mostly focused on molecular condensed phase systems. It is an open source free software licensed under the GNU GPL, is platform independent, and does not require any external libraries. Nine years after the original publication of TRAVIS, we highlight some of the recent new functions and features in this article. At the same time, we shortly present some of the underlying algorithms in TRAVIS, which contribute to make trajectory analysis more efficient. Some modern visualization techniques such as Sankey diagrams are also demonstrated. Many analysis functions are implemented, covering structural analyses, dynamical analyses, and functions for predicting vibrational spectra from molecular dynamics simulations. While some of the analyses are known since several decades, others are very recent. For example, TRAVIS has been used to compute the first ab initio predictions in the literature of bulk phase vibrational circular dichroism spectra, bulk phase Raman optical activity spectra, and bulk phase resonance Raman spectra within the last few years.TRAVIS ("Trajectory Analyzer and Visualizer") is a program package for post-processing and analyzing trajectories from molecular dynamics and Monte Carlo simulations, mostly focused on molecular condensed phase systems. It is an open source free software licensed under the GNU GPL, is platform independent, and does not require any external libraries. Nine years after the original publication of TRAVIS, we highlight some of the recent new functions and features in this article. At the same time, we shortly present some of the underlying algorithms in TRAVIS, which contribute to make trajectory analysis more efficient. Some modern visualization techniques such as Sankey diagrams are also demonstrated. Many analysis functions are implemented, covering structural analyses, dynamical analyses, and functions for predicting vibrational spectra from molecular dynamics simulations. While some of the analyses are known since several decades, others are very recent. For example, TRAVIS has been used to compute the first ab initio predictions in the literature of bulk phase vibrational circular dichroism spectra, bulk phase Raman optical activity spectra, and bulk phase resonance Raman spectra within the last few years. TRAVIS (“Trajectory Analyzer and Visualizer”) is a program package for post-processing and analyzing trajectories from molecular dynamics and Monte Carlo simulations, mostly focused on molecular condensed phase systems. It is an open source free software licensed under the GNU GPL, is platform independent, and does not require any external libraries. Nine years after the original publication of TRAVIS, we highlight some of the recent new functions and features in this article. At the same time, we shortly present some of the underlying algorithms in TRAVIS, which contribute to make trajectory analysis more efficient. Some modern visualization techniques such as Sankey diagrams are also demonstrated. Many analysis functions are implemented, covering structural analyses, dynamical analyses, and functions for predicting vibrational spectra from molecular dynamics simulations. While some of the analyses are known since several decades, others are very recent. For example, TRAVIS has been used to compute the first ab initio predictions in the literature of bulk phase vibrational circular dichroism spectra, bulk phase Raman optical activity spectra, and bulk phase resonance Raman spectra within the last few years. |
| Author | Gehrke, S. Kirchner, B. Brehm, M. Thomas, M. |
| Author_xml | – sequence: 1 givenname: M. surname: Brehm fullname: Brehm, M. organization: Institut für Chemie, Martin-Luther-Universität Halle–Wittenberg – sequence: 2 givenname: M. surname: Thomas fullname: Thomas, M. organization: Institut für Chemie, Martin-Luther-Universität Halle–Wittenberg – sequence: 3 givenname: S. surname: Gehrke fullname: Gehrke, S. organization: Mulliken Center for Theoretical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn – sequence: 4 givenname: B. surname: Kirchner fullname: Kirchner, B. organization: Mulliken Center for Theoretical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/32357781$$D View this record in MEDLINE/PubMed |
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| CODEN | JCPSA6 |
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| Snippet | TRAVIS (“Trajectory Analyzer and Visualizer”) is a program package for post-processing and analyzing trajectories from molecular dynamics and Monte Carlo... TRAVIS ("Trajectory Analyzer and Visualizer") is a program package for post-processing and analyzing trajectories from molecular dynamics and Monte Carlo... |
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| SubjectTerms | Algorithms Computer simulation Dichroism Freeware Molecular dynamics Optical activity Post-processing Raman spectra Trajectory analysis Vibrational spectra |
| Title | TRAVIS—A free analyzer for trajectories from molecular simulation |
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