Exploring Potential Energy Surfaces
The Fast Marching Method(FMM) developed in this group is used to fill up the potential surface by exploring points with the lowest potential value. The algorithm developed expands a wavefront of points to proceed from the reactant to the product. Shepard interpolation, with moving least squares to fit the higher order derivatives of the potential can be used to reduce the number of calculations. The minimum energy path (MEP) can be obtained once the calculation is done. Also we use the quadratic string method (QSM) and the sequential quadratic programming method (SQPM) which start from an initial guess of the MEP and proceed as an optimization algorithm.
Fortran 90 QSM code in internal coordinates (serial version).
Fortran 90 QSM code in internal coordinates (parallel MPI version).
C version of SQPM (serial/parallel MPI version).
Fortran 90 code for FMM (serial version).
Para-MEAD
A parameterized version of linearized Poisson-Boltzmann solver MEAD (Macroscopic Electrostatics with Atomic Detail). Instructions for compiling the program and running it can be found in the README file in the main directory. Instructions for running para-MEAD can be found in the file examples/README. Many of the PDB files from the paper can be found in this directory.
Para-freq
A program for parameterizing force constants based on the frequencies. This is based on the paper
The software is available with a tutorial.
Para Freq v1.3 with Zn(II)(imidazole)3(SCH3)]+ as an example