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Serial_Replica_Exchange
Replica exchange method (REM) is a powerful method for speeding up the sampling of conformational states of proteins with rough energy landscapes, where stable conformational states can be separated by large energy barriers. The usual REM requires that different replicas run synchronously. Serial replica exchange (SREM), a method that is equivalent to standard REM in terms of efficiency, yet runs asynchronously on a distributed network of computers. This unique feature enables it to study the protein folding on the distributed computing environment or even on your desktop at home (for small systems and coarse graining models). SIMTK "Serial_Replica_Exchange" has the feature to do the serial replica exchange. Since it is based on Gromacs-3.1.4, all the tools and functions of Gromacs are still usable. Right now, it is only implemented for the Linux version.
SREM_1.0
Jan 22, 2007

Download Links

Mar 26, 2007
1 MB
Linux
Source code
A FFTW Library compatiable with SREM code

Mar 26, 2007
35 MB
Linux
Source code
The souce code for serial replica exchange based on Gromacs package. Version 1.0

Documentation Links

Mar 27, 2007
The documentation for serial replica exchange v1.0, read this first

Mar 27, 2007
A tutorial for running SREM simulations on the Fs-peptide system.

PLEASE CITE THESE PAPERS

Huang X, Bowman GR, Pande VS. (2008). Journal of Chemical Physics, 128,205106 (2008)

M. Hagen, B. Kim, P. Liu, R.A. Frisener, B.J.Berne, J. Phys. Chem. B(in press), 2007 (2007)

Erik Lindahl, Berk Hess and David van der Spoel, J. Mol. Mod. 7, 306-317 (2001)

H.J.C. Berendsen, D. van der Spoel and R. van Drunen, Comp. Phys. Comm. 91, 43-56 (1995)


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