NMscatt: a program for calculating inelastic scattering from large biomolecular systems using classical force-field simulations

Abstract

Computational tools for normal mode analysis, which are widely used in physics and materials science problems, are designed here in a single package called NMscatt (Normal Modes & scattering) that allows arbitrarily large systems to be handled. The package allows inelastic neutron and X-ray scattering observables to be calculated, allowing comparison with experimental data produced at large scale facilities. Various simplification schemes are presented for analyzing displacement vectors, which are otherwise too complicated to understand in very large systems. Program summary Title of program:NMscatt Catalogue identifier:ADZA_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADZA_v1_0.html Program obtainable from:CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions:no No. of lines in distributed program, including test data, etc.:573 535 No. of bytes in distributed program, including test data, etc.:4 516 496 Distribution format:tar.gz Programming language:FORTRAN 77 Computer:x86 PC Operating system:GNU/Linux, UNIX RAM:Depends on the system size to be simulated Word size:32 or 64 bits Classification:16.3 External routines:LAPACK Nature of problem: Normal mode analysis, phonons calculation, derivation of incoherent and coherent inelastic scattering spectra. Solution method: Full diagonalization (producing eigen-vectors and eigen-values) of dynamical matrix which is obtained from potential energy function derivation using finite difference method. Running time: About 7 hours per one k-point evaluation in sampling all modes dispersion curves for a system containing 3550 atoms in the unit cell on AMD Athlon 64 X2 Dual Core Processor 4200+.