Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields. The method is applied mostly in chemical physics, materials science, and biophysics.
Visual Molecular Dynamics (VMD) is a molecular modelling and visualization computer program. VMD is developed mainly as a tool to view and analyze the results of molecular dynamics simulations. It also includes tools for working with volumetric data, sequence data, and arbitrary graphics objects. Molecular scenes can be exported to external rendering tools such as POV-Ray, RenderMan, Tachyon, Virtual Reality Modeling Language (VRML), and many others. Users can run their own Tcl and Python scripts within VMD as it includes embedded Tcl and Python interpreters. VMD runs on Unix, Apple Mac macOS, and Microsoft Windows. VMD is available to non-commercial users under a distribution-specific license which permits both use of the program and modification of its source code, at no charge.
Martin Karplus is an Austrian and American theoretical chemist. He is the Director of the Biophysical Chemistry Laboratory, a joint laboratory between the French National Center for Scientific Research and the University of Strasbourg, France. He is also the Theodore William Richards Professor of Chemistry, emeritus at Harvard University. Karplus received the 2013 Nobel Prize in Chemistry, together with Michael Levitt and Arieh Warshel, for "the development of multiscale models for complex chemical systems".
Charm++ is a parallel object-oriented programming paradigm based on C++ and developed in the Parallel Programming Laboratory at the University of Illinois at Urbana–Champaign. Charm++ is designed with the goal of enhancing programmer productivity by providing a high-level abstraction of a parallel program while at the same time delivering good performance on a wide variety of underlying hardware platforms. Programs written in Charm++ are decomposed into a number of cooperating message-driven objects called chares. When a programmer invokes a method on an object, the Charm++ runtime system sends a message to the invoked object, which may reside on the local processor or on a remote processor in a parallel computation. This message triggers the execution of code within the chare to handle the message asynchronously.
Free energy perturbation (FEP) is a method based on statistical mechanics that is used in computational chemistry for computing free energy differences from molecular dynamics or Metropolis Monte Carlo simulations.
This is a list of computer programs that are predominantly used for molecular mechanics calculations.
The Center for Simulation of Advanced Rockets (CSAR) is an interdisciplinary research group at the University of Illinois at Urbana-Champaign, and is part of the United States Department of Energy's Advanced Simulation and Computing Program. CSAR's goal is to accurately predict the performance, reliability, and safety of solid propellant rockets.
Molecular modeling on GPU is the technique of using a graphics processing unit (GPU) for molecular simulations.
CP2K is a freely available (GPL) quantum chemistry and solid state physics program package, written in Fortran 2008, to perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. It provides a general framework for different methods: density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW) via LDA, GGA, MP2, or RPA levels of theory, classical pair and many-body potentials, semi-empirical and tight-binding Hamiltonians, as well as Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid schemes relying on the Gaussian Expansion of the Electrostatic Potential (GEEP). The Gaussian and Augmented Plane Waves method (GAPW) as an extension of the GPW method allows for all-electron calculations. CP2K can do simulations of molecular dynamics, metadynamics, Monte Carlo, Ehrenfest dynamics, vibrational analysis, core level spectroscopy, energy minimization, and transition state optimization using NEB or dimer method.
In computer software, Orac is a classical molecular dynamics program, to simulate complex molecular systems at the atomistic level. In 1989-1990, the code was written originally by Massimo Marchi during his stay at International Business Machines (IBM), Kingston (USA). In 1995, the code was developed further at the Centre européen de calcul atomique et moléculaire (CECAM). It is written in the programming language Fortran. In 1997, it was released under a GNU General Public License (GPL). The latest release of Orac may be run in parallel using the standard Message Passing Interface (MPI) libraries, allowing replica exchange simulations, multiple walkers metadynamics simulations and multiple steered molecular dynamics nonequilibrium trajectories.
Martin Gruebele is a German-born American physical chemist and biophysicist who is currently James R. Eiszner Professor of Chemistry, Professor of Physics, Professor of Biophysics and Computational Biology at the University of Illinois Urbana-Champaign, where he is the principal investigator of the Gruebele Group.
Tachyon is a parallel/multiprocessor ray tracing software. It is a parallel ray tracing library for use on distributed memory parallel computers, shared memory computers, and clusters of workstations. Tachyon implements rendering features such as ambient occlusion lighting, depth-of-field focal blur, shadows, reflections, and others. It was originally developed for the Intel iPSC/860 by John Stone for his M.S. thesis at University of Missouri-Rolla. Tachyon subsequently became a more functional and complete ray tracing engine, and it is now incorporated into a number of other open source software packages such as VMD, and SageMath. Tachyon is released under a permissive license.
Laxmikant (Sanjay) V. Kale is the director of the Parallel Programming Laboratory (PPL) and a professor of computer science at the University of Illinois at Urbana-Champaign. He also holds department affiliations with the Beckman Institute and the Department of Mechanical and Industrial Engineering at Illinois.
Newton-X is a general program for molecular dynamics simulations beyond the Born-Oppenheimer approximation. It has been primarily used for simulations of ultrafast processes in photoexcited molecules. It has also been used for simulation of band envelops of absorption and emission spectra.
Zaida Ann "Zan" Luthey-Schulten is the William and Janet Lycan Professor of Chemistry at the University of Illinois at Urbana-Champaign. She was promoted to professor in 2004. She is also involved with the NASA Astrobiology Institute.
Klaus Schulten was a German-American computational biophysicist and the Swanlund Professor of Physics at the University of Illinois at Urbana-Champaign. Schulten used supercomputing techniques to apply theoretical physics to the fields of biomedicine and bioengineering and dynamically model living systems. His mathematical, theoretical, and technological innovations led to key discoveries about the motion of biological cells, sensory processes in vision, animal navigation, light energy harvesting in photosynthesis, and learning in neural networks.
Nancy Makri is the Edward William and Jane Marr Gutgsell Endowed Professor of Chemistry and Physics at the University of Illinois Urbana–Champaign, where she is the principal investigator of the Makri Research Group for the theoretical understanding of condensed phase quantum dynamics. She studies theoretical quantum dynamics of polyatomic systems, and has developed methods for long-time numerical path integral simulations of quantum dissipative systems.
PLUMED is an open-source library implementing enhanced-sampling algorithms, various free-energy methods, and analysis tools for molecular dynamics simulations. It is designed to be used together with ACEMD, AMBER, DL_POLY, GROMACS, LAMMPS, NAMD, OpenMM, ABIN, CP2K, i-PI, PINY-MD, and Quantum ESPRESSO, but it can also be used to together with analysis and visualization tools VMD, HTMD, and OpenPathSampling.
In the context of chemistry and molecular modelling, the Interface force field (IFF) is a force field for classical molecular simulations of atoms, molecules, and assemblies up to the large nanometer scale, covering compounds from across the periodic table. It employs a consistent classical Hamiltonian energy function for metals, oxides, and organic compounds, linking biomolecular and materials simulation platforms into a single platform. The reliability is often higher than that of density functional theory calculations at more than a million times lower computational cost. IFF includes a physical-chemical interpretation for all parameters as well as a surface model database that covers different cleavage planes and surface chemistry of included compounds. The Interface Force Field is compatible with force fields for the simulation of primarily organic compounds and can be used with common molecular dynamics and Monte Carlo codes. Structures and energies of included chemical elements and compounds are rigorously validated and property predictions are up to a factor of 100 more accurate relative to earlier models.
