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Fast, parallel MD, CUDA Proprietary, free academic use, source code Beckman Institute: NWChem: No No Yes Yes No No Yes No No High-performance computational chemistry software, includes quantum mechanics, molecular dynamics and combined QM-MM methods Free open source, Educational Community License version 2.0 NWChem: Protein Local Optimization ...
Radius of gyration (in polymer science)(, unit: nm or SI unit: m): For a macromolecule composed of mass elements, of masses , =1,2,…,, located at fixed distances from the centre of mass, the radius of gyration is the square-root of the mass average of over all mass elements, i.e.,
It is often useful to give the gyrofrequency a sign with the definition = or express it in units of hertz with =. For electrons, this frequency can be reduced to , = (/).. In cgs-units the gyroradius = | | and the corresponding gyrofrequency = | | include a factor , that is the velocity of light, because the magnetic field is expressed in units [] = / /.
The most basic kinds of simulation are minimizing a given structure and production runs of a molecular dynamics trajectory. More advanced features include free energy perturbation (FEP), quasi-harmonic entropy estimation, correlation analysis and combined quantum, and quantum mechanics – molecular mechanics ( QM/MM ) methods.
Q is a computer software package for molecular dynamics (MD) simulation (current release: Q6). Unlike other MD codes, it has specialized since its conception (Marelius et al. 1998) on three specific types of free energy calculations.
Other simulation methods (such as replica exchange) are supported through a plug-in-based infrastructure, which also allows users to develop their own simulation algorithms and models. Desmond is also available in a graphics processing unit (GPU) accelerated version that is about 60-80 times faster than the central processing unit (CPU) version.
Advanced Simulation Library - open-source hardware accelerated multiphysics simulation software. ASCEND - open-source equation-based modelling environment. Cantera - chemical kinetics package. Celestia - a 3D astronomy program. CP2K - Open-source ab-initio molecular dynamics program. DWSIM - an open-source CAPE-OPEN compliant chemical process ...
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.