Programs in Physics & Physical Chemistry
|[Licence| Download | New Version Template] aeda_v1_0.tar.gz(3595 Kbytes)|
|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.|
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.
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.
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.
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