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Molecular Dynamics Programs for simulation of biomolecular systems Amber-Amber
Molecular Dynamics Programs for simulation of biomolecular systems Amber-HPC Systems Co., Ltd.

Molecular Dynamics Programs for simulation of biomolecular systems Amber
HPC Systems Co., Ltd.

About This Product

■Product overview

Amber is a set of force fields for molecular dynamics (MD) calculations of biomolecules, developed by P. A. Kollman's group at the University of California, and a set of MD programs for simulating these force fields. It is currently maintained and managed by a group led by D. A. Case of Rutgers University in the United States. The program group is broadly divided into input preparation program, simulation program, and result analysis program. Amber16, which is optimized not only for GPUs but also for the latest Xeon Phi processors, was released in April 2016.

■Features

The implementation of solvent theory 3D-RISM and the Hamiltonian replica exchange method has increased the precision of calculations and made it possible to calculate on larger systems. It is also used in structure-based drug discovery. It is possible to reproduce the intracellular environment and quantitatively determine the binding free energy. It is also possible to collaborate with GAUSSIAN.

■Amber's basic functions

・Free energy calculation using free energy perturbation method, thermodynamic integration method, etc. ・Free energy calculation in solvent ・Energy minimization calculation ・MD simulation ・Calculation of interatomic distances and angles ・Calculation of temperature factor (B-factor) ・Calculation of root mean square deviation (RMSd) to measure structural changes and structural fluctuations

■New features of Amber12

・Compatible with various force fields ・Improved accuracy of calculation of solvation free energy ・Improved sampling efficiency ・Easy update procedure - Closely linked with quantum computing ・Implementation of sander functionality to both CPU and GPU versions of pemd ・Free energy calculations that change the Hamiltonian model are now more accurate ・Simulation using experimental information

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    Molecular Dynamics Programs for simulation of biomolecular systems Amber

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1 Models of Molecular Dynamics Programs for simulation of biomolecular systems Amber

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Amber

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