Services

ABINIT

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 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 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

How to Run Batch Job

How to Run Batch Job Using PBS in HPC Cluster The PBS Pro job scheduler is a powerful cluster management tool that enables users to make full use of the computing resources available in HPC. Some useful features that can be found in PBS job scheduler include: • Ability to

Registration Guide

Registration GuideRegistering for an account via HPC Portal The HPC Portal is open to all NUS staff and students who have a valid NUS-ID account. When accessing HPC Portal for the first time, users will be prompted to fill up an online registration form and submit it electronically for approval.

Parallel Computing

Parallel ComputingIntroduction The following four types of parallel computing are available for you to consider depending on the nature of your computational work and your preference. Model Description OpenMP Running a program by multithreading method on multiple cores within a compute node MPI Running a program on multiple cores either

Gromacs

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

GaussView

GaussView GaussView 5 is the latest release of GaussView from Gaussian. You may use it to build molecules and visualize data from Gaussian. It is available on, MobileVisLab. To start up GaussView 5 : > gv5 Kindly note and comply with the following terms of our Gaussian/GaussView academic license.  Your usage of Gaussian/GaussView implies