Computer Physics Communications Program LibraryPrograms in Physics & Physical Chemistry |

[Licence| Download | New Version Template] aeda_v1_0.tar.gz(3595 Kbytes) | ||
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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_0Distribution 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. |

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