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.
Highlights
Within the last few decades, the methods of molecular dynamics (MD) and Monte Carlo simulations have become a central part of computational chemistry and physics
Most dynamical analyses should not be applied to Monte Carlo simulations, as there exists no physical time in standard Monte Carlo approaches
The magnetic dipole moment cannot be obtained from a Born–Oppenheimer molecular dynamics (BOMD) simulation, as magnetic moments arise from electric currents, and the Born–Oppenheimer approximation does not account for electric currents
Summary
Within the last few decades, the methods of molecular dynamics (MD) and Monte Carlo simulations have become a central part of computational chemistry and physics. It is a commonly known phenomenon that many working groups from the field of computational science use their own inhouse scripts and codes to evaluate and analyze simulation trajectories These codes all have their specific scopes, strengths, and limitations, and despite being developed in independent groups, many methods and algorithms are for sure almost equivalent in all these tools. We are going to shortly introduce some of the underlying algorithms that are typically invisible for users but are, very important to achieve the desired efficiency and accuracy of trajectory analyses This manuscript is structured as follows: After a discussion of general features of TRAVIS in Sec. II, we will discuss specific features from the fields of structural, dynamical, and spectroscopic analyses in Secs.
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