HPC

Nmag Nmag is a micromagnetic simulation package. It has been developed at the University of Southampton with substantial contributions from Hans Fangohr, Thomas Fischbacher, Matteo Franchin. It is released under the GNU GPL. Features in brief: • based on finite elements (suitable for non-cuboidal structures) • problem description in Python, therefore

MrBayes MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes’s theorem. The posterior probability distribution of trees

Molden Molden is a pre- and post-processing program of molecular and electronic structures. It can display molecular density from the ab initio packages GAMESS and GAUSSIAN, and the Semi-Empirical packages Mopac/Ampac. Molden is capable of displaying molecular orbitals, the electron density and the molecular minus atomic density. It can write

MODELLER What is MODELLER? MODELLER is a program for comparative protein structure modeling by satisfaction of spatial restraints. It is used for homology or comparative modeling of protein 3D structures. Where can I find information of MODELLER? MODELLER is maintained by Ben Webb at the Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry,

MeepIntroduction Meep implements the finite-difference time-domain (FDTD) method for computational electromagnetism.  The current version installed in SVU is 1.0.3.  More details on the Meep software can be found at the developer’s website. Running a Parallel Meep job in SVU Meep is currently only available on atlas4 cluster.  To run a 4-cpu

Gamess GAMESS(General Atomic and Molecular Electronic Structure System) is a general ab initio quantum chemistry package. The current version available in our systems is 5 Dec 2014 version. To run GAMESS: • Create one subfolder (scr) in your home directory • Create one subfolder in /hpctmp2/scr with your userid as the

Autodock AutoDock is is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. It has applications in: • X-ray crystallography • structure-based drug design • lead optimization • virtual screening (HTS) •