Software...
- Parallel Packmol
Parallel Packmol is a parallel version of Packmol, developed using OpenMP.
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 package is compatible with input files of PDB, TINKER, XYZ and MOLDY formats.
For more information about Parallel Packmol, software download, or instalation instructions click here
- Parallel PUMA
Parallel PUMA is a parallel version of PUMA (Pointwise Unconstrained Minimization Approach), developed using MPI.
The software PUMA implements an unconstrained formulation of the nonlinear programming model, wich solves the problem of estimating the thickness and the optical constants of thin filmes using transmission data. This formulation is solved using a method based on repeated calls to a recently introduced unconstrained minimization algorithm.
The problem of estimating the thickness and the optical constants of thin films using transmission data only is very challenging from the mathematical point of view, and has a technological and an economic importance. In many cases it represents a very ill-conditioned inverse problem with many local-nonglobal solutions. In a recent publication, we proposed nonlinear programming models for solving this problem. Well-known software for linearly constrained optimization was used with success for this purpose.