Replica-exchange method using the generalized effective potential.

Soonmin Jang; Seokmin Shin; Youngshang Pak

doi:10.1103/physrevlett.91.058305

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Replica-exchange method using the generalized effective potential.

Soonmin Jang·Seokmin Shin·Youngshang Pak

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Abstract

We propose an effective scheme for fast conformational searches by combining the replica exchange method (REM) with the generalized effect potential concept. The present method introduces the "q" value from the effective potential as a coupling parameter. It is found that the new method not only requires a much smaller number of replicas than the conventional REM, but also makes it possible to perform effective conformational sampling of complex systems with correct distributions maintained. The advantage of the present method has been demonstrated with in vacuo alanine dipeptide using a molecular dynamics simulation.

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Computer Simulation Dipeptides Models, Chemical Protein Conformation Thermodynamics Vacuum Journal Article Research Support, Non-U.S. Gov't

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Soonmin Jang, Seokmin Shin, Youngshang Pak. 2003-08-01. Replica-exchange method using the generalized effective potential.. https://doi.org/10.1103/physrevlett.91.058305

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