Programs in Physics & Physical Chemistry
|[Licence| Download | New Version Template] aexw_v1_0.tar.gz(112876 Kbytes)|
|Manuscript Title: MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations|
|Authors: Sandra Vergara-Perez, Marcelo Marucho|
|Program title: MPBEC|
|Catalogue identifier: AEXW_v1_0|
Distribution format: tar.gz
|Journal reference: Comput. Phys. Commun. 198(2016)179|
|Programming language: Matlab R2010a and higher versions.|
|Computer: Any computer at least with 2.5 GHz speed.|
|Operating system: Windows, Linux Fedora, and Mac OSX.|
|RAM: At least 2 GB of free memory.|
|Keywords: Poisson-Boltzmann equation, biomolecular electrostatic calculations, mean electrostatic potential, Matlab software, Graphical user interface.|
|Classification: 3, 10.|
External routines: Java, Jmol, pdb2pqr, Propka.
Nature of problem:
Numerical solution of the linearized PB equation.
MPBEC uses sparse matrix calculations and iterative linear solvers (gmres, minres, and bicgstab) to solve the discretized (box method) linear PB equation. The stability and the convergence of these iterative solvers is improved by using the incomplete LU factorization which generates pre-conditioner matrices L (lower triangular matrix) and U (upper triangular matrix) at low computational cost.
MPBEC incorporates a GUI to provide non-experts in computational biophysics a user-friendly and intuitive tool to obtain biomolecular electrostatic calculations. The GUI provides helpful information about how to fill out the input data by moving the mouse pointer over the corresponding text or blank box. The GUI tests all the input data before running MPBEC to make sure that the solver is properly configured and facilitates the user with the pre- and post-analysis of the biomolecular calculations.
MPBEC checks available and required RAM memory before allocation to alert users when the available RAM memory is insufficient to perform the required calculations depending basically on the number of grid points and the size and number of atoms of the biomolecule(s). Therefore, MPBEC might be used with lower RAM memory and processor speed conditions than those mentioned above.
The software runs on single processor computers at low-to-moderate computational cost depending on the computer performance, the biomolecule size, the grid resolution, and required calculations.
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