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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 [] = / /.
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.,
High Performance MD, highly flexible, Python scriptable Free open source MIT: OpenMM: Orac: No No Yes Yes No Yes No Yes No Molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomic level Free open source: Orac download page: NAMD + VMD: Yes Yes Yes Yes No Yes I Yes Yes Fast, parallel MD, CUDA
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.
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.
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.
Verification and validation of computer simulation models is conducted during the development of a simulation model with the ultimate goal of producing an accurate and credible model. [ 1 ] [ 2 ] "Simulation models are increasingly being used to solve problems and to aid in decision-making.
Molecular Dynamics of Mixtures (MDynaMix) is a computer software package for general purpose molecular dynamics to simulate mixtures of molecules, interacting by AMBER- and CHARMM-like force fields in periodic boundary conditions.