Title

SMMP v. 3.0-Simulating proteins and protein interactions in Python and Fortran

Document Type

Article

Publication Date

3-15-2008

Abstract

We describe a revised and updated version of the program package SMMP. SMMP is an open-source FORTRAN package for molecular simulation of proteins within the standard geometry model. It is designed as a simple and inexpensive tool for researchers and students to become familiar with protein simulation techniques. SMMP 3.0 sports a revised API increasing its flexibility, an implementation of the Lund force field, multi-molecule simulations, a parallel implementation of the energy function, Python bindings, and more. Program summary: Title of program:SMMP. Catalogue identifier:ADOJ_v3_0. Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADOJ_v3_0.html. Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland. Licensing provisions:Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html. Programming language used:FORTRAN, Python. No. of lines in distributed program, including test data, etc.:52 105. No. of bytes in distributed program, including test data, etc.:599 150. Distribution format:tar.gz. Computer:Platform independent. Operating system:OS independent. RAM:2 Mbytes. Classification:3. Does the new version supersede the previous version?:Yes. Nature of problem:Molecular mechanics computations and Monte Carlo simulation of proteins. Solution method:Utilizes ECEPP2/3, FLEX, and Lund potentials. Includes Monte Carlo simulation algorithms for canonical, as well as for generalized ensembles. Reasons for new version:API changes and increased functionality. Summary of revisions:Added Lund potential; parameters used in subroutines are now passed as arguments; multi-molecule simulations; parallelized energy calculation for ECEPP; Python bindings. Restrictions:The consumed CPU time increases with the size of protein molecule. Running time:Depends on the size of the simulated molecule. © 2007 Elsevier B.V. All rights reserved.

Publication Title

Computer Physics Communications

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