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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 ...
Tinker, previously stylized as TINKER, is a suite of computer software applications for molecular dynamics simulation. The codes provide a complete and general set of tools for molecular mechanics and molecular dynamics, with some special features for biomolecules. The core of the software is a modular set of callable routines which allow ...
Jmol is computer software for molecular modelling of chemical structures in 3 dimensions. [2] It is an open-source Java viewer for chemical structures in 3D [3]. The name originated from ava (the programming language) + [mol]ecules, and also the mol file format. JSmol is an implementation in JavaScript of the functionality of Jmol. [4]
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 ...
Molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids. Linux, macOS, Windows: Common Public 1.0 GenoViz Integrated Genome Browser: Java-based desktop genome browser: Linux, macOS, Windows: Common Public 1.0 GenoViz InterMine
Most types of molecular wires are derived from organic molecules. One naturally occurring molecular wire is DNA.Prominent inorganic examples include polymeric materials such as Li 2 Mo 6 Se 6 [1] and Mo 6 S 9−x I x, [2] [3] [4] [Pd 4 (CO) 4 (OAc) 4 Pd(acac) 2], [5] and single-molecule extended metal atom chains (EMACs) which comprise strings of transition metal atoms directly bonded to each ...
charmm – The name of the program (or script which runs the program) on the computer system being used. filename.inp – A text file which contains the CHARMM commands. It starts by loading the molecular topologies (top) and force field (par). Then one loads the molecular structures' Cartesian coordinates (e.g. from PDB files).
A notable 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.