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Concept

Comparison of software for molecular mechanics modeling

Summary

This is a list of computer programs that are predominantly used for molecular mechanics calculations.

Official source

https://en.wikipedia.org/wiki/Comparison_of_software_for_molecular_mechanics_modeling

About this result

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Related publications (4)

i-PI 2.0: A universal force engine for advanced molecular simulations

Michele Ceriotti, David Mark Wilkins, Bingqing Cheng, Venkat Kapil, Riccardo Petraglia, Gareth Aneurin Tribello, Mariana Rossi Carvalho, Benjamin Aaron Helfrecht, Robert Horst Meissner, Alice Cuzzocrea, Sébastien Pierre Bienvenue, Przemyslaw Juda, Wei Fang

Progress in the atomic-scale modeling of matter over the past decade has been tremendous. This progress has been brought about by improvements in methods for evaluating interatomic forces that work by either solving the electronic structure problem explicitly, or by computing accurate approximations of the solution and by the development of techniques that use the Born-Oppenheimer (BO) forces to move the atoms on the BO potential energy surface. As a consequence of these developments it is now possible to identify stable or metastable states, to sample configurations consistent with the appropriate thermodynamic ensemble, and to estimate the kinetics of reactions and phase transitions. All too often, however, progress is slowed down by the bottleneck associated with implementing new optimization algorithms and/or sampling techniques into the many existing electronic-structure and empirical-potential codes. To address this problem, we are thus releasing a new version of the i-PI software. This piece of software is an easily extensible framework for implementing advanced atomistic simulation techniques using interatomic potentials and forces calculated by an external driver code. While the original version of the code (Ceriotti et al., 2014) was developed with a focus on path integral molecular dynamics techniques, this second release of i-PI not only includes several new advanced path integral methods, but also offers other classes of algorithms. In other words, i-PI is moving towards becoming a universal force engine that is both modular and tightly coupled to the driver codes that evaluate the potential energy surface and its derivatives. Program summary Program Title: i-PI Program Files doi: http://dx.doLorg/10.17632/x792grbm9g.1 Licensing provisions: GPLv3, MIT Programming language: Python External routines/libraries: NumPy Nature of problem: Lowering the implementation barrier to bring state-of-the-art sampling and atomistic modeling techniques to ab initio and empirical potentials programs. Solution method: Advanced sampling methods, including path-integral molecular dynamics techniques, are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic coordinates from the Python interface, and to return the forces and energy that are used to integrate the equations of motion, optimize atomic geometries, etc. Restrictions: This code does not compute interatomic potentials, although the distribution includes sample driver codes that can be used to test different techniques using a few simple model force fields. (C) 2018 Elsevier B.V. All rights reserved.

ELSEVIER SCIENCE BV2019

Towards a Composite Benchmark Method for the Aqueous Solvation Free Energies of Organic Compounds

Daniel David Sadowsky

Water is ubiquitous in the biosphere, and the difficulty of rigorously treating the effects of aqueous solvation currently limits the widespread use of computational methods in many areas of environmental chemistry. We propose an approach to benchmark calculations of aqueous free energies of solvation based on molecular dynamics simulation which is derived from first principles, statistical mechanically complete, and systematically improvable. The approach partitions the solvation free energy into the free energies of solvent density change, solvent cavity organization, and solvent-solute interaction, each of which is computed from first principles. A composite approach is considered for the calculation of the contributions of quantum nuclear effects to solvation free energies and the contributions of electron correlation and relativistic effects to solvent-solute interactions.

2015

What Singles Out the G[8-5]C Intrastrand DNA Cross-Link? Mechanistic and Structural Insights from Quantum Mechanics/Molecular Mechanics Simulations

Chandan Patel

Naturally occurring intrastrand oxidative crosslink lesions have proven to be a potent source of endogenous DNA damage. Among the variety of lesions that can be formed and have been identified, G[8-5]C damage (in which the C8 atom of a guanine is covalently bonded to the CS atom of a nearby cytosine belonging to the same strand) occurs with a low incidence yet takes on special importance because of its high mutagenicity. Hybrid Car-Parrinello molecular dynamics simulations, rooted in density functional theory and coupled to molecular mechanics, have been performed to shed light on the cyclization process. The activation free energy of the reacting subsystem embedded in a solvated dodecamer is estimated to be similar to 12.4 kcal/mol, which is similar to 3 kcal/mol higher than the value for the prototypical G[8-5m]T lesion inferred employing the same theoretical framework [Garrec, 3., Patel, C., Rothlisberger, U., and Dumont, E. (2012) J. Am. Chem. Soc. 134, 2111-2119]. This study also situates the G[8-5m]mC lesion at an intermediate activation free energy (similar to 10.5 kcal/mol). The order of reactivity in DNA (T-center dot > mC(center dot) > C-center dot) is reversed compared to that in the reacting subsystems in the gas phase (C-center dot > mC(center dot) > T-center dot), stressing the crucial role of the solvated B-helix environment. The results of our simulations also characterize a more severe distortion for G[8-5]C than for methylene-bridged intrastrand cross-links.

Amer Chemical Soc2013

Related people (3)

Michele Ceriotti, Matteo Dal Peraro, Ursula Röthlisberger

Related units (4)

Laboratory of Computational Chemistry and Biochemistry

Laboratory of Computational Science and Modelling

Prof. Dal Peraro Group

Related concepts (23)

Molecule editor

A molecule editor is a computer program for creating and modifying representations of chemical structures. Molecule editors can manipulate chemical structure representations in either a simulated two-dimensional space or three-dimensional space, via 2D computer graphics or 3D computer graphics, respectively. Two-dimensional output is used as illustrations or to query chemical databases. Three-dimensional output is used to build molecular models, usually as part of molecular modelling software packages.

Comparison of software for molecular mechanics modeling

This is a list of computer programs that are predominantly used for molecular mechanics calculations.

Parallel tempering

Parallel tempering, in physics and statistics, is a computer simulation method typically used to find the lowest energy state of a system of many interacting particles. It addresses the problem that at high temperatures, one may have a stable state different from low temperature, whereas simulations at low temperatures may become "stuck" in a metastable state. It does this by using the fact that the high temperature simulation may visit states typical of both stable and metastable low temperature states.

Related courses (4)

BIO-315: Structural biology

The main focus of this course is on the molecular interactions defining the structure, dynamics and function of biological systems. The principal experimental and computational techniques used in stru

CH-351: Molecular dynamics and Monte-Carlo simulation

Introduction to molecular dynamics and Monte-Carlo simulation methods.

BIO-110: Bio-organic chemistry

The aim of the course is to provide a chemical understanding and intuition to decipher and predict chemical processes in living systems.

Related lectures (40)

Large-Scale Computing Future

Explores large-scale computing, excitation processes in molecules, and the importance of accurate correlation energies in chemistry.

Molecular dynamics under constraints

Explores molecular dynamics simulations under holonomic constraints, focusing on numerical integration and algorithm formulation.

QM/MM Hybrid Methods

Explores the integration of quantum mechanics and molecular mechanics in computational chemistry using CP2K software.

Related MOOCs (2)

Path Integral Methods in Atomistic Modelling

The course provides an introduction to the use of path integral methods in atomistic simulations. The path integral formalism allows to introduce quantum mechanical effects on the equilibrium and (ap

Path Integral Methods in Atomistic Modelling

The course provides an introduction to the use of path integral methods in atomistic simulations. The path integral formalism allows to introduce quantum mechanical effects on the equilibrium and (ap

i-PI 2.0: A universal force engine for advanced molecular simulations

ELSEVIER SCIENCE BV2019