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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 ...
Likewise, these force fields may be used within other molecular dynamics programs that support them. In 2009, a general force field for drug-like molecules (CGenFF) was introduced. It "covers a wide range of chemical groups present in biomolecules and drug-like molecules, including a large number of heterocyclic scaffolds". [ 12 ]
This is a list of computer programs that use Monte Carlo methods for molecular modeling. Abalone classical Hybrid MC; BOSS classical; CASINO quantum [1] Cassandra classical [2] CP2K; FEASST classical [3] GOMC classical [4] Internal_Coordinate_Mechanics ICM by MolSoft classical [5] MacroModel classical; Materials Studio classical; ms2 [6] [7] [8 ...
An important advantage of QM/MM methods is their efficiency. The cost of doing classical molecular mechanics (MM) simulations in the most straightforward case scales as O(N 2), where N is the number of atoms in the system. This is mainly due to electrostatic interactions term (every particle interacts with everything else).
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 ]
Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. [1] The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies.
Metadynamics (MTD; also abbreviated as METAD or MetaD) is a computer simulation method in computational physics, chemistry and biology.It is used to estimate the free energy and other state functions of a system, where ergodicity is hindered by the form of the system's energy landscape.
The direct simulation Monte Carlo algorithm is like molecular dynamics in that the state of the system is given by the positions and velocities of the particles, {,}, for =, …,. Unlike molecular dynamics, each particle in a DSMC simulation represents F N {\displaystyle F_{N}} molecules in the physical system that have roughly the same ...