All-Atom Steered Molecular Dynamics Simulations of Large Proteins in a Small Water Box

Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics.

Molecular dynamics (MD) simulations of ions (K+, Na+, Ca2+ and Cl-) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parametrized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration....

All-Atom Simulations of Proteins

The successful deciphering of the human genome has highlighted an old challenge in protein science: For most of the resolved protein sequences, we do not know the corresponding structures and functions. Neither do we understand in detail the mechanism by which a protein folds into its biologically active form. Computer experiments offer one way to evaluate the sequence–structure relationship an...

All-atom generalized-ensemble simulations of small proteins.

We give an overview of some generalized-ensemble techniques that have proven successful in all-atom simulations of proteins. We show that these techniques enable efficient investigations of secondary structure formation and folding in peptides and small proteins. Results are presented for various alanine-based artificial peptides and a small protein, the 36-residued villin headpiece subdomain (...

High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing

Although molecular dynamics simulation methods are useful in the modeling of macromolecular systems, they remain computationally expensive, with production work requiring costly high-performance computing (HPC) resources. We review recent innovations in accelerating molecular dynamics on graphics processing units (GPUs), and we describe GPUGRID, a volunteer computing project that uses the GPU r...

Coarse grained potential functions for proteins derived from all-atom explicit-solvent molecular dynamics simulations