Program title: MPBEC
Catalogue identifier: AEXW_v1_0
Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEXW_v1_0.html
Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland
Licensing provisions: UTSA license
No. of lines in distributed program, including test data, etc.: 1505214
No. of bytes in distributed program, including test data, etc.: 115585507
Distribution format: tar.gz
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.
Classification: 3, 10.
External routines: Java, Jmol, pdb2pqr, Propka.
Nature of problem: Numerical solution of the linearized PB equation.
Solution method: 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 are improved by using the incomplete LU factorization which generates pre-conditioner matrices user=111111111&_pii=S0010465515003288&_rdoc=1&_issn=00104655&md5=a58ae06cb46db987542c3df59226b942" title="Click to view the MathML source">L (lower triangular matrix) and user=111111111&_pii=S0010465515003288&_rdoc=1&_issn=00104655&md5=1c89001cefc2bd0f65e96c182558a9fb" title="Click to view the MathML source">U (upper triangular matrix) at low computational cost.
Unusual features: 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.
Additional comments: 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 distribution file for this program is over 115 Mbytes and therefore is not delivered directly when download or Email is requested. Instead a html file giving details of how the program can be obtained is sent.
Running time: 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.