Application Software

VMD VMD (Visual Molecular Dynamics) is an open source molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to

Siesta Siesta (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. Siesta 4.1.3 is currently installed in the HPC systems. To submit Siesta jobs, login to

Quantum Espresso Quantum Espresso is an integrated suite of computer codes for electronic-structure calculation and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. The parallel version Quantum Espresso 5.2 is made available in all clusters. You can use the following template script to submit

NAMD NAMD is a open source parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. NAMD uses the popular molecular graphics program VMD for simulation

Materials StudioIntroduction Materials Studio is a complete modeling and simulation software package designed to allow researchers in materials science and chemistry to predict and understand the relationships of a material’s atomic and molecular structure with its properties and behavior. Obtaining Materials Studio Please get in touch with us via nTouch (see

Compiling/ Running User-Written Programs The following compilers, debuggers and performance tuning tools are available on HPC systems. Check their man pages or the subsequent sessions in this user guide for the usage and options. Compilers icc Intel C/C++ Compiler ifort Intern Fortran Compiler gcc, g++ GNU project C and C++

ABINIT ABINIT is a software package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. abinit-8.0.8 version is installed in the

Amber Amber is a software package for molecular dynamics simulations, particularly for proteins, nucleic acids and carbohydrates. It’s also a family of force field for molecular dynamics of biomolecules. The Amber software package is distributed by UCSF subject to a licensing agreement. Amber 14 CPU version is installed in /app1/centos6.3/gnu/apps/amber14. The

LAMMPS LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics program from Sandia National Laboratories. It has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator

GROMACS GROMACS is a highly optimized open source molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids that have a lot of complicated bonded interactions. Gromacs 5.0.4 is compiled and installed in the HPC cluster using different compilers and different levels of acceleration. Please use the following