Available Instruments for Analyzing Molecular Dynamics Trajectories



I. V. Likhachev1, 2, N. K. Balabaev2, O. V. Galzitskaya1, *
1 Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
2 Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia


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© Likhachev et al.; Licensee Bentham Open.

open-access license: This is an open access article licensed under the terms of the Creative Commons Attribution-Non-Commercial 4.0 International Public License (CC BY-NC 4.0) (https://creativecommons.org/licenses/by-nc/4.0/legalcode), which permits unrestricted, non-commercial use, distribution and reproduction in any medium, provided the work is properly cited.

* Address correspondence to this author at the Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia; Tel. (+7)4967-318275; E-mail: ogalzit@vega.protres.ru


Abstract

Molecular dynamics trajectories are the result of molecular dynamics simulations. Trajectories are sequential snapshots of simulated molecular system which represents atomic coordinates at specific time periods. Based on the definition, in a text format trajectory files are characterized by their simplicity and uselessness. To obtain information from such files, special programs and information processing techniques are applied: from molecular dynamics animation to finding characteristics along the trajectory (versus time). In this review, we describe different programs for processing molecular dynamics trajectories. The performance of these programs, usefulness for analyses of molecular dynamics trajectories, strong and weak aspects are discussed.

Keywords: MD trajectory, MD program, silico experiment, analysis, protein conformation.