[Debichem-devel] Bug#941726: ITP: packmol -- Initial configurations for Molecular Dynamics Simulations by packing optimization

[Drew Parsons]

Package: wnpp
Severity: wishlist
Owner: Drew Parsons <dparsons at debian.org>

* Package name    : packmol
  Version         : 18.169
  Upstream Author : Leandro Martínez, José Mario Martínez, Ernesto Birgin
* URL             : http://m3g.iqm.unicamp.br/packmol/
* License         : MIT
  Programming Lang: fortran90
  Description     : Initial configurations for Molecular Dynamics Simulations by packing optimization

Packmol creates an initial point for molecular dynamics simulations by
packing molecules in defined regions of space. The packing guarantees
that short range repulsive interactions do not disrupt the
simulations.

The great variety of types of spatial constraints that can be
attributed to the molecules, or atoms within the molecules, makes it
easy to create ordered systems, such as lamellar, spherical or tubular
lipid layers.

The user must provide only the coordinates of one molecule of each
type, the number of molecules of each type and the spatial constraints
that each type of molecule must satisfy.

The package is compatible with input files of PDB, TINKER, XYZ and
MOLDY formats.

See http://m3g.iqm.unicamp.br/packmol for more information.

References

Please always cite one of the following references in publications for
which Packmol was useful:

L Martinez, R Andrade, EG Birgin, JM Martinez, Packmol: A package for
building initial configurations for molecular dynamics simulations.
Journal of Computational Chemistry, 30, 2157-2164, 2009.
(http://www3.interscience.wiley.com/journal/122210103/abstract)

JM Martinez, L Martinez, Packing optimization for the automated
generation of complex system's initial configurations for molecular
dynamics and docking. Journal of Computational Chemistry, 24, 819-825,
2003. (http://www3.interscience.wiley.com/journal/104086246/abstract)



This package complements existing molecular dynamics software such as
lammps, gromacs, cp2k and others, providing tools for filling a volume
with solvent molecules.

This area of application is more specialised and therefore the package
can be team-maintained under debichem rather than debian-science.

Drew