# Difference between revisions of "Apbsplugin"

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M. Holst and F. Saied, ''Numerical solution of the nonlinear Poisson-Boltzmann equation: Developing more robust and efficient methods.'' '''J. Comput. Chem.''' 16, 337-364, 1995. <br> | M. Holst and F. Saied, ''Numerical solution of the nonlinear Poisson-Boltzmann equation: Developing more robust and efficient methods.'' '''J. Comput. Chem.''' 16, 337-364, 1995. <br> | ||

For PMG (the multigrid solver): <br> | For PMG (the multigrid solver): <br> | ||

− | M. Holst, ''Adaptive numerical treatment of elliptic systems on manifolds.'' '''Advances in Computational Mathematics 15''', 139-191, 2001. [http://dx.doi.org/10.1023/A:1014246117321 | + | M. Holst, ''Adaptive numerical treatment of elliptic systems on manifolds.'' '''Advances in Computational Mathematics 15''', 139-191, 2001. |

+ | [http://dx.doi.org/10.1023/A:1014246117321 doi:10.1023/A:1014246117321] <br> | ||

For FEtk (the finite element solver): <br> | For FEtk (the finite element solver): <br> | ||

− | R. Bank and M. Holst, ''A New Paradigm for Parallel Adaptive Meshing Algorithms.'' '''SIAM Review 45''', 291-323, 2003. [http://dx.doi.org/10.1137/S003614450342061 | + | R. Bank and M. Holst, ''A New Paradigm for Parallel Adaptive Meshing Algorithms.'' '''SIAM Review 45''', 291-323, 2003. |

− | doi:10.1137/S003614450342061] | + | [http://dx.doi.org/10.1137/S003614450342061 doi:10.1137/S003614450342061] |

=== MALOC === | === MALOC === |

## Revision as of 06:29, 6 December 2011

## Contents

## Software requirements

Register use of the software. This will the authors able to require funding for further development.

Register here, it takes 1 minutes: http://www.poissonboltzmann.org/apbs/downloads

### Windows

Download **APBS.msi** from: http://sourceforge.net/projects/apbs/files/apbs/

### Ubuntu

APBS are in the repository: http://packages.ubuntu.com/search?keywords=apbs

MALOC are in the repository: http://packages.ubuntu.com/search?keywords=libmaloc1

## References and LICENSES

### APBS

When using the APBS, you are "obligated" to register your use of the software. This will the authors able to require funding for further development.

Register here, it takes 1 minutes: http://www.poissonboltzmann.org/apbs/downloads

Please acknowledge your use of APBS by citing:

Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. *Electrostatics of nanosystems: application to microtubules and the ribosome.*
**Proc. Natl. Acad. Sci. USA 98**, 10037-10041 2001. doi:10.1073/pnas.181342398

Please acknowledge your use of the Holst group software by citing:

M. Holst and F. Saied, *Multigrid solution of the Poisson-Boltzmann equation.* **J. Comput. Chem. 14**, 105-113, 1993.

M. Holst and F. Saied, *Numerical solution of the nonlinear Poisson-Boltzmann equation: Developing more robust and efficient methods.* **J. Comput. Chem.** 16, 337-364, 1995.

For PMG (the multigrid solver):

M. Holst, *Adaptive numerical treatment of elliptic systems on manifolds.* **Advances in Computational Mathematics 15**, 139-191, 2001.
doi:10.1023/A:1014246117321

For FEtk (the finite element solver):

R. Bank and M. Holst, *A New Paradigm for Parallel Adaptive Meshing Algorithms.* **SIAM Review 45**, 291-323, 2003.
doi:10.1137/S003614450342061

### MALOC

Please acknowledge the use of MALOC and FETK by citing:

M. Holst, *Adaptive numerical treatment of elliptic systems on manifolds.* **Advances in Computational Mathematics**, 15 (2001), pp. 139-191.

Copyright and Terms of Use:

GNU General Public License: http://www.gnu.org/copyleft/gpl.html

```
This version of MALOC is distributed under the following guidelines:
MALOC (Minimal Abstraction Layer for Object-oriented C)
Copyright (C) 1994-2010 Michael Holst
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
```