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338 Database entries



Amber


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OS: Linux, Windows, Mac, ...

Methods: MM, QM/MM, free Energy



Features:

Force fields: Many new force field types are available, including new water and ion models; updated nucleic acid and carbohydrate parameters; parallel support for the AMOEBA polarizable potentials of Ren and Ponder; and improved empirical valence bond (EVB) models that can be used to construct approximate potentials for chemical reactions.

QM/MM Simulations: Amber 10 now allows DFTB calculations in periodic solvent boxes or with the generalized Born solvation model. Codes are faster and (modestly) parallel.

Adaptively biased simulations can be used to accelerate sampling and free energy convergence.

Path integral molecular dynamics simulations can be used to sample equilibrium canonical distributions using quantum dynamics rather than Newton's equations for nuclear motion. Both equilibrium and kinetic isotope effects can be estimated via thermodynamic integration over mass. Rate constants can be estimated using the Quantum Instanton model, and approximate quantum time-correlation functions are available using Ring Polymer MD or Centroid MD.

A new suite of conformational clustering tools is available in ptraj.

New free energy tools significantly simplify the setup of mutational changes in proteins, allowing for both "single" and "dual" topologies. A soft-core potential facility aids sampling in systems where atoms are appearing or disappearing, with no need for the creation of artificial dummy atoms.

Updates to the replica exchange methods, including improvements to the standard replica exchange code and support for exchange methods with a non-Boltzmann reservoir, or in which a hybrid solvent model is used to reduce the number of replicas required for large systems in explicit solvent.

Significant improvements in speed and parallel scaling are available in an expanded pmemd program, which now includes generalized Born capability, and support for off-center charges (as in TIP4P or TIP5P).

Full integration of the low-mode (LMOD) search tools based on following low-frequency normal modes.


Link: http://ambermd.org/


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