packmol
Initial configurations for Molecular Dynamics Simulations
Command lineScience
Not tested on a device yet. What that means
Commands in the package
packmolsolvate.tcl
About packmol
From Debian's package 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)
From Debian's description of the packmol package, under that package's license.
Dependencies
Depends on
libc6libgfortran5
Recommends
On x86-64 it also needs libgcc-s1.
Related apps
- gromacsMolecular dynamics simulator, with building and analysis toolsCommand line
- lammpsMolecular Dynamics SimulatorCommand line
GDPC Molecular Dynamic SimulatorVisualize molecular dynamic simulations- quantum-espressoElectronic-Structure and Ab-Initio Molecular Dynamics SuiteCommand line
- cp2kAb Initio Molecular DynamicsCommand line
- mpgraficMPI version of N-body initial conditions grafic packageCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the packmol package, under that package's license.
- Description: Debian's description of the packmol package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
More in About the catalog.