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Manuscript Title: REACH: A Program for Coarse-Grained Biomolecular Simulation
Authors: Kei Moritsugua, Jeremy C. Smith
Program title: REACH
Catalogue identifier: AEDA_v1_0
Distribution format: tar.gz
Journal reference: Comput. Phys. Commun. 180(2009)1188
Programming language: FORTRAN 77.
Computer: x86 PC.
Operating system: GNU/Linux, SUSE and Red Hat.
RAM: Depends on the system size to be calculated
Word size: 32 or 64 bits
Keywords: REACH, coarse-grained force field, Molecular Dynamics (MD) simulation, elastic network model (ENM).
PACS: 87.14.Ee, 87.15.Aa, 31.15.Qg.
Classification: 3.

External routines: LAPACK, BLAS

Nature of problem:
A direct calculation of force field for residue-scale coarse-grained biomolecular simulation derived from atomistic molecular dynamics trajectory.

Solution method:
A variance-covariance matrix and the associated Hessian (second-derivative) matrix are calculated from an atomistic molecular dynamics trajectory of single-domain protein internal motion and the off-diagonal Hessian matrix is fitted to that of a residue-scale elastic network model. The resulting force constants for the residue pair interactions are expressed as model functions as a function of pairwise distance.

Running time:
Depends on the system size and the number of MD trajectory frames used. The test run provided with the distribution takes only a few seconds to execute.