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High-performance computational chemistry software, includes quantum mechanics, molecular dynamics and combined QM-MM methods Free open source, Educational Community License version 2.0 NWChem: Protein Local Optimization Program: No Yes Yes Yes Yes No No No No Helix, loop, and side chain optimizing, fast energy minimizing Proprietary: PLOP wiki ...
Conventional computational chemistry methods often struggle with the complex quantum mechanical equations, particularly due to the exponential growth of a quantum system's wave function. Quantum computational chemistry addresses these challenges using quantum computing methods , such as qubitization and quantum phase estimation , which are ...
The difference between states A and B may be in the atom types involved, in which case the ΔF obtained is for "mutating" one molecule onto another, or it may be a difference of geometry, in which case one obtains a free-energy map along one or more reaction coordinates. This free-energy map is also known as a potential of mean force (PMF).
The fundamental difference between a calculator and computer is that a computer can be programmed in a way that allows the program to take different branches according to intermediate results, while calculators are pre-designed with specific functions (such as addition, multiplication, and logarithms) built in.
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.
Semi-empirical quantum chemistry methods are based on the Hartree–Fock formalism, but make many approximations and obtain some parameters from empirical data. They are very important in computational chemistry for treating large molecules where the full Hartree–Fock method without the approximations is too expensive.
Cheminformatics (also known as chemoinformatics) refers to the use of physical chemistry theory with computer and information science techniques—so called "in silico" techniques—in application to a range of descriptive and prescriptive problems in the field of chemistry, including in its applications to biology and related molecular fields.
The invariance properties of molecular descriptors can be defined as the ability of the algorithm for their calculation to give a descriptor value that is independent of the particular characteristics of the molecular representation, such as atom numbering or labeling, spatial reference frame, molecular conformations, etc. Invariance to molecular numbering or labeling is assumed as a minimal ...