Towards fast, rigorous and efficient conformational sampling of biomolecules: Advances in accelerated molecular dynamics

Doshi U, Hamelberg D Biochim. Biophys. Acta 2015 May;1850(5):878-888 PMID: 25153688 Abstract BACKGROUND: Accelerated molecular dynamics (aMD) has been proven to be a powerful biasing method for enhanced sampling of biomolecular conformations on general-purpose computational platforms. Biologically important long timescale events that are beyond the reach of standard molecular dynamics can be accessed without losing […]

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Twenty-five years of nucleic acid simulations

Cheatham TE, Case DA Biopolymers 2013 Dec;99(12):969-77 PMID: 23784813 Abstract We present a brief, and largely personal, history of computer simulations of DNA and RNA oligonucleotides, with an emphasis on duplex structures and the Amber force fields. Both explicit and implicit solvent models are described, and methods for estimating structures, thermodynamics and mechanical properties of […]

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Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics

Pierce LC, Salomon-Ferrer R, Augusto F de Oliveira C, McCammon JA, Walker RC J Chem Theory Comput 2012 Sep;8(9):2997-3002 PMID: 22984356 Abstract In this work, we critically assess the ability of the all-atom enhanced sampling method accelerated molecular dynamics (aMD) to investigate conformational changes in proteins that typically occur on the millisecond time scale. We […]

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Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

Götz AW, Williamson MJ, Xu D, Poole D, Le Grand S, Walker RC J Chem Theory Comput 2012 May;8(5):1542-1555 PMID: 22582031 Abstract We present an implementation of generalized Born implicit solvent all-atom classical molecular dynamics (MD) within the AMBER program package that runs entirely on CUDA enabled NVIDIA graphics processing units (GPUs). We discuss the […]

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The Amber biomolecular simulation programs

Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM, Onufriev A, Simmerling C, Wang B, Woods RJ J Comput Chem 2005 Dec;26(16):1668-88 PMID: 16200636 Abstract We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was […]

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Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules

Hamelberg D, Mongan J, McCammon JA J Chem Phys 2004 Jun;120(24):11919-29 PMID: 15268227 Abstract Many interesting dynamic properties of biological molecules cannot be simulated directly using molecular dynamics because of nanosecond time scale limitations. These systems are trapped in potential energy minima with high free energy barriers for large numbers of computational steps. The dynamic […]

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Force fields for protein simulations

Ponder JW, Case DA Adv. Protein Chem. 2003;66:27-85 PMID: 14631816 Abstract

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