We present TRAVIS (“TRajectory Analyzer and VISualizer”), a free program package for analyzing and visualizing Monte Carlo and molecular dynamics trajectories. The aim of TRAVIS is to collect as many analyses as possible in one program, creating a powerful tool and making it unnecessary to use many different programs for evaluating simulations. This should greatly rationalize and simplify the workflow of analyzing trajectories. TRAVIS is written in C++, open-source freeware and licensed under the terms of the GNU General Public License (GPLv3). It is easy to install (platform independent, no external libraries) and easy to use. In this article, we present some of the algorithms that are implemented in TRAVIS - many of them widely known for a long time, but some of them also to appear in literature for the first time. All shown analyses only require a standard MD trajectory as input data.

We review several methods for the calculation of vibrational spectra from ab initio molecular dynamics (AIMD) simulations and we present a new implementation in the trajectory analyzer TRAVIS. In particular, we show mass-weighted power spectra, infrared spectra, and Raman spectra with corresponding depolarization ratios, which are based on time-correlation functions of velocities, dipole moments, and polarizabilities, respectively. Using the four organic molecules methanol, acetone, nitromethane, and pinacol as test systems, we compare the spectra from AIMD simulations of the isolated molecules in gas phase to static calculations relying on the harmonic approximation and to experimental spectra recorded in a nonpolar solvent. The AIMD approach turns out to give superior results when anharmonicity effects are of particular importance. Using the example of methanol, we demonstrate the application to bulk phase systems, which are not directly accessible by static calculations, but for which the AIMD spectra also provide a very good approximation to experimental data. Finally, we investigate the influence of simulation time and temperature in the AIMD on the resulting spectra.

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.

We carried out classical molecular dynamics simulations with a standard and two quantum chemistry based charge sets to study the ionic liquid 1-n-butyl-3-methylimidazolium bromide, [C(4)C(1)im][Br]. We split the cation up into different charge groups and found that the total charge and the charge distribution in the imidazolium ring are completely different in the three systems while the total charge of the butyl chain is much better conserved between the methods. For comparison, the spatial distribution functions and the radial distribution functions as well as different time correlation functions were calculated. For the structural properties we obtained a good agreement between the standard and one of the two quantum chemistry based sets, while the results from the second quantum chemistry based set led to a completely different picture. The opposite was observed for the dynamic properties, which agree well between the standard set and the second quantum chemistry based set, whereas the dynamics in the first charge set obtained by quantum chemistry calculations proceeded much too slow, which is not obvious from the total charge. We observed, that the structure of the butyl chain is mostly unaffected by the choice of the charge set. This is an indirect proof for separation into ionic parts and nonpolar domains. A second focus of the article is the investigation of dynamical heterogeneity and the ion cages. Therefore, we analyzed the reorientational dynamics in the three systems and at five different temperatures in system with the standard charge set. Generally speaking, we detected four different time domains. The fastest movement can be found for the continuous hydrogen bond and the nearest neighbor ion pair dynamics. In the second time domain the movement of the butyl chain took place. The third time domain consisted in the increasing movement of the imidazolium ring as well as in the continuous distortion of an ion cage, i.e., the departure of one of the several counterions from the central ion's first shell, and the intermittent hydrogen bond dynamics. The remaining domain involves the translational displacement of the ions.