REACH: A program for coarse-grained biomolecular simulation

Abstract

REACH ( Realistic Extension Algorithm via Covariance Hessian) is a program package for residue-scale coarse-grained biomolecular simulation. The program calculates the force constants of a residue-scale elastic network model in single-domain proteins using the variance–covariance matrix obtained from atomistic molecular dynamics simulation. Secondary-structure dependence of the force constants is integrated. The method involves self-consistent, direct mapping of atomistic simulation results onto a coarse-grained force field in an efficient automated procedure without requiring iterative fits and avoiding system dependence. Program summary Program title: REACH Catalogue identifier: AEDA_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEDA_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 42 244 No. of bytes in distributed program, including test data, etc.: 3 682 118 Distribution format: tar.gz 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 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.