MolTwister – a molecular systems construction, manipulation and statistical mechanical calculation tool

Abstract

To perform molecular dynamics (MD) simulations, Monte Carlo (MC) simulations, quantum mechanical (QM) electronic structure calculations, or similar atomistic calculations, it is necessary to first construct and define the molecular system of interest. This involves creating an initial configuration of atoms, where MD and MC simulations require forcefield assignments, for example in the form of non-bonded, bonded, angular and dihedral potentials. Once simulations or calculations have been performed, large sets of data are available (often several gigabytes). These contain atomic trajectories and other relevant static or dynamic information, from which static and dynamic properties (such as density profiles, vibrational density of states and velocity autocorrelation functions) can be obtained through statistical mechanical calculations. MolTwister is an open source software platform that addresses the construction of molecular systems, basic 3D visualization of these, the generation of input files for selected MD packages, as well as calculation of properties from atomistic simulation data. It also contains a GPU accelerated MD simulator suited for smaller tasks such as molecular thermalization. The software package is written in C++14 and can be used as a basis for further development, where efforts have been made to make access to underlying functionality easy. Moreover, it supports Python, where scripts have access to the majority of program functionality. Program summaryProgram Title: MolTwisterCPC Library link to program files:https://doi.org/10.17632/ph6pwst9mn.1Developer's repository link:http://moltwister.comLicensing provisions: GPLv3 or laterProgramming language: C++14Nature of problem: Lack of SW tools for easy construction of complex molecular systems, as well as tools enabling analysis of long molecular trajectories.Solution method: Developed command line tool with associated 3D view, where molecular construction commands can be executed in complex manners through a Python interface. The program also has commands for analysis of molecular data that process one molecular time-frame at a time, thus enabling analysis of long molecular trajectories. Moreover, the program structure is designed for easy implementation of new commands by other researchers.Additional comments including restrictions and unusual features: Supported file formats: xyz, pdb, mtt (MolTwister trajectory), dcd, xtc, qepos, python, script (MolTwister scripts)Supported MD engines: HOOMD-blue, LAMMPS, MolTwister internal (moldyn)