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Molecule builder-editor for Windows, Linux, Unix, and macOS. All source code is licensed under the GNU General Public License (GPL) version 2. Supported languages include: Chinese , English , French , German , Italian , Russian , Spanish , and Polish .
They may also include density functional theory (DFT), molecular mechanics or semi-empirical quantum chemistry methods. The programs include both open source and commercial software. Most of them are large, often containing several separate programs, and have been developed over many years.
Examples of nanowires include inorganic molecular nanowires (Mo 6 S 9−x I x, Li 2 Mo 6 Se 6), which can have a diameter of 0.9 nm and be hundreds of micrometers long. Other important examples are based on semiconductors such as InP, Si, GaN, etc., dielectrics (e.g. SiO 2 ,TiO 2 ), or metals (e.g. Ni, Pt).
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 ...
The CHARMM molecular dynamics package [4] can read and write a number of standard chemical and biochemical file formats; however, the CARD (coordinate) and PSF (protein structure file) are largely unique to CHARMM. The CARD format is fixed-column-width, resembles the PDB format, and is used exclusively for storing atomic coordinates.
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 ...
GAMESS (US) also has a series of fragmentation methods that allow the user to target larger molecular systems by partitioning a large molecule into smaller, more feasible fragments. Examples are the fragment molecular orbital (FMO) method, the Effective Fragment Potential (EFP) method, and the Effective Fragment Molecular Orbital method (EFMO).
SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is an original method and its computer program implementation, to efficiently perform electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.
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