Serial Replica Exchange

Hagen, Morten; Kim, Byungchan; Liu, Pu; Friesner, Richard A.; Berne, B. J.

doi:10.1021/jp064479e

Cited by 39 publications

(69 citation statements)

References 33 publications

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“…The SREM algorithm, 24 a serial version of the REM, is designed to run asynchronously on a worldwide distributed computing environment such as FAH. 34 We will first review the original REM.…”

Section: A Serial Replica Exchangementioning

confidence: 99%

“…Recently, Hagen et alnoticed that in REM energy is the only property involved in the detailed balance condition, They derived the SREM based on this property. 24 In SREM, PEDFs, P͑E , T n ͒, are stored at different temperatures. The algorithm works as follows: A single replica is propagated with MC or MD at temperature T n using a single processor.…”

Section: ͑2͒mentioning

confidence: 99%

“…Hagen et alsuggest that the PEDFs be updated iteratively until they are stationary. 24 We apply SREM on a distributed computing network to study the helix-coil transition. In Sec.…”

Section: ͑2͒mentioning

confidence: 99%

“…The above simulations were first equilibrated for 2.5 ns at different initial temperatures. In a subsequent updating phase, slightly different from what was suggested by Hagen et al, 24 we continued updating the PEDFs, though the updates became less frequent with time. The PEDFs were updated every 40 ns for about 40 iterations at first, then every 400 ns for about 20 iterations, and at last every 1000 ns.…”

Section: Simulation Detailsmentioning

confidence: 99%

“…23 Recently, Hagen et al proposed another method called serial replica exchange method ͑SREM͒ that is suitable for distributed computing. 24 In SREM, a single, independent simulation performs a random walk in temperature space by making regular attempts to change temperatures. The transition probability for this move is determined by one potential energy from the simulation and a second one from a prestored potential energy distribution function ͑PEDF͒ at the new temperature.…”

Section: Introductionmentioning

confidence: 99%

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Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment

Huang

Bowman

Pande

2008

The Journal of Chemical Physics

114

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We have implemented the serial replica exchange method ͑SREM͒ and simulated tempering ͑ST͒ enhanced sampling algorithms in a global distributed computing environment. Here we examine the helix-coil transition of a 21 residue ␣-helical peptide in explicit solvent. For ST, we demonstrate the efficacy of a new method for determining initial weights allowing the system to perform a random walk in temperature space based on short trial simulations. These weights are updated throughout the production simulation by an adaptive weighting method. We give a detailed comparison of SREM, ST, as well as standard MD and find that SREM and ST give equivalent results in reasonable agreement with experimental data. In addition, we find that both enhanced sampling methods are much more efficient than standard MD simulations. The melting temperature of the Fs peptide with the AMBER99 potential was calculated to be about 310 K, which is in reasonable agreement with the experimental value of 334 K. We also discuss other temperature dependent properties of the helix-coil transition. Although ST has certain advantages over SREM, both SREM and ST are shown to be powerful methods via distributed computing and will be applied extensively in future studies of complex bimolecular systems.

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Section: A Serial Replica Exchangementioning

confidence: 99%

Section: ͑2͒mentioning

confidence: 99%

“…Hagen et alsuggest that the PEDFs be updated iteratively until they are stationary. 24 We apply SREM on a distributed computing network to study the helix-coil transition. In Sec.…”

Section: ͑2͒mentioning

confidence: 99%

Section: Simulation Detailsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment

Huang

Bowman

Pande

2008

The Journal of Chemical Physics

114

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Asynchronous replica exchange for molecular simulations

2007

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An asynchronous implementation of the replica exchange method that addresses some of the limitations of conventional synchronous replica exchange implementations is presented. In asynchronous replica exchange pairs of processors initiate and perform temperature replica exchanges independently from the other processors, thereby removing the need for processor synchronization found in conventional synchronous implementations. Illustrative calculations on a molecular system are presented that show that asynchronous replica exchange, contrary to the synchronous implementation, is able to utilize at nearly top efficiency loosely coupled pools of processors with heterogeneous speeds, such as those found in computational grids and CPU scavenging environments. It is also shown that employing non nearest-neighbor temperature exchanges, which are straightforward to implement within the asynchronous algorithm, can lead to faster temperature equilibration across processors.

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How hot? Systematic convergence of the replica exchange method using multiple reservoirs

2009

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We have devised a systematic approach to converge a replica exchange molecular dynamics simulation by dividing the full temperature range into a series of higher temperature reservoirs and a finite number of lower temperature subreplicas. A defined highest temperature reservoir of equilibrium conformations is used to help converge a lower but still hot temperature subreplica, which in turn serves as the high-temperature reservoir for the next set of lower temperature subreplicas. The process is continued until an optimal temperature reservoir is reached to converge the simulation at the target temperature. This gradual convergence of subreplicas allows for better and faster convergence at the temperature of interest and all intermediate temperatures for thermodynamic analysis, as well as optimizing the use of multiple processors. We illustrate the overall effectiveness of our multiple reservoir replica exchange strategy by comparing sampling and computational efficiency with respect to replica exchange, as well as comparing methods when converging the structural ensemble of the disordered Abeta(21-30) peptide simulated with explicit water by comparing calculated Rotating Overhauser Effect Spectroscopy intensities to experimentally measured values.

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Serial Replica Exchange

Cited by 39 publications

References 33 publications

Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment

Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment

Asynchronous replica exchange for molecular simulations

How hot? Systematic convergence of the replica exchange method using multiple reservoirs

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