# Peptide Folding Kinetics from Replica Exchange Molecular Dynamics

Source: [Peptide Folding Kinetics from Replica Exchange Molecular Dynamics](<https://www.sota2.com/research/paper/68fa24292c2a3760193a0060>)

Collection index: [llms.txt](<https://www.sota2.com/research/llms.txt>)

Data updated: 2025-10-28T13:52:42.160Z

Authors: Nicolae-Viorel Buchete, Gerhard Hummer

Published: 2007-10-29T21:11:39.000Z

## Abstract

We show how accurate kinetic information, such as the rates of protein folding and unfolding, can be extracted from replica-exchange molecular dynamics (REMD) simulations. From the brief and continuous trajectory segments between replica exchanges, we estimate short-time propagators in conformation space and use them to construct a master equation. For a helical peptide in explicit water, we determine the rates of transitions both locally between microscopic conformational states and globally for folding and unfolding. We show that accurate rates in the ~1/(100 ns) to ~1/(1 ns) range can be obtained from REMD with exchange times of 5 ps, in excellent agreement with results from long equilibrium molecular dynamics.

## Recorded benchmark results

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## Original sources and implementation

[Original paper](<https://arxiv.org/abs/0710.5533>)

[PDF](<https://arxiv.org/pdf/0710.5533.pdf>)