Gast ::
| Hauptseite > Publikationsdatenbank > SMMP v. 3.0 - Simulating proteins and protein interactions in Python and Fortran |
| Hauptseite > Publikationsdatenbank > SMMP v. 3.0 - Simulating proteins and protein interactions in Python and Fortran |
| Journal Article | PreJuSER-62832 |
; ; ;
2008
North Holland Publ. Co.
Amsterdam
This record in other databases: 
Please use a persistent id in citations: doi:10.1016/j.cpc.2007.11.004
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 summaryTitle of program: SMMPCatalogue identifier: ADOJ_v3_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADOLv3-0.htmlProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlProgramming language used: FORTRAN, PythonNo. of lines in distributed program, including test data, etc.: 52 105No. of bytes in distributed program, including test data, etc.: 599 150Distribution format: tar.gzComputer: Platform independentOperating system: OS independentRAM: 2 MbytesClassification: 3Does the new version supersede the previous version?: YesNature 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. (C) 2007 Elsevier B.V. All rights reserved.
Keyword(s): J ; FORTRAN package (auto) ; protein folding (auto) ; Monte Carlo (auto) ; minimization (auto) ; generalized-ensemble simulations (auto) ; Python (auto)
|
The record appears in these collections: |