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High performance GPU-accelerated ab initio molecular dynamics and TD/DFT software package for very large molecular or even nanoscale systems. Runs on NVIDIA GPUs and 64-bit Linux, has heavily optimized CUDA code. Proprietary, trial licenses available PetaChem LLC: TINKER: I Yes Yes Yes Yes I I Yes Yes Software tools for molecular design-Tinker ...
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.,
Along with the molecular dynamics program, the Desmond software also includes tools for minimizing and energy analysis, both of which can be run efficiently in a parallel environment. Force fields parameters can be assigned using a template-based parameter assignment tool called Viparr . [ 11 ]
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.
Nanoscale Molecular Dynamics (NAMD, formerly Not Another Molecular Dynamics Program) [1] is computer software for molecular dynamics simulation, written using the Charm++ parallel programming model (not to be confused with CHARMM). It is noted for its parallel efficiency and is often used to simulate large systems (millions of atoms). [2]
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.