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Computational methodologies that couple the dynamical evolution of a set of replicated copies of a system of interest offer powerful and flexible approaches to characterize complex molecular processes. Such multiple copy algorithms (MCAs) can be used to enhance sampling, compute reversible work and free energies, as well as refine transition pathways.… (More)

- Mikolai Fajer, Donald Hamelberg, J. Andrew McCammon
- 2008

Accelerated molecular dynamics (AMD) is an efficient strategy for accelerating the sampling of molecular dynamics simulations, and observable quantities such as free energies derived on the biased AMD potential can be re-weighted to yield results consistent with the original, unmodified potential. In conventional AMD the reweighting procedure has an… (More)

- Mehrnoosh Arrar, Cesar Augusto F. de Oliveira, Mikolai Fajer, William Sinko, J. Andrew McCammon
- 2013

Free energy governs the equilibrium extent of many biological processes. High barriers separating free energy minima often limit the sampling in molecular dynamics (MD) simulations, leading to inaccurate free energies. Here, we demonstrate enhanced sampling and improved free energy calculations, relative to conventional MD, using windowed accelerated MD… (More)

- Kathleen E. Rogers, Juan Manuel Ortiz-Sánchez, Riccardo Baron, Mikolai Fajer, César Augusto F. de Oliveira, J. Andrew McCammon
- 2013

We use thermodynamic integration (TI) and explicit solvent molecular dynamics (MD) simulation to estimate the absolute free energy of host−guest binding. In the unbound state, water molecules visit all of the internally accessible volume of the host, which is fully hydrated on all sides. Upon binding of an apolar guest, the toroidal host cavity is fully… (More)

- Mikolai Fajer, Jérôme Hénin, Benoˆıt Roux, Christophe Chipot
- 2015

This tutorial sets out to determine the free-energy difference between two conformational states of a short, terminally blocked peptide, N–acetyl–N –methylalaninamide, along a meaningful transition pathway. To reach this objective, use will be made of the string method with swarm of trajectories. Starting from a guess, rectilinear transition pathway… (More)

Replica exchange accelerated molecular dynamics (REXAMD) is a method that enhances conformational sampling while retaining at least one replica on the original potential, thus avoiding the statistical problems of exponential reweighting. In this article, we study three methods that can combine the data from the accelerated replicas to enhance the estimate… (More)

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