Bio Excel is based on improving three aspects of biomolecular research.
Firstly, improving the performance and scalability of the most commonly used software, such as GROMACS ( HADDOCK ( and CPMD (org), to take advantage of next-gen HPC systems and the expected increase in the amount of data produced.
It’s also important to improve how easy it is for users to access and use these types of software.
Bio Excel aims to provide customisable workflow environments, which will allow relatively novice HPC/HTC users take advantage of the analysis software provided in ways that suit their specific research.In addition to this, hands-on training and public webinars are already underway, aiming to teach researchers best practices and how to best utilise the software and resources available.In this manuscript, we will introduce a recently developed program GPView, which can be used for wave function analysis and visualization.The wave function analysis module can calculate and generate 3D cubes for various types of molecular orbitals and electron density related with electronic excited states, such as natural orbitals, natural transition orbitals, natural difference orbitals, hole-particle density, detachment-attachment density and transition density.The visualization module of GPView can display molecular and electronic (iso-surfaces) structures.
It is also able to animate single trajectories of molecular dynamics and non-adiabatic excited state molecular dynamics using the data stored in existing files.
There are also other utilities help to extract and process the output of quantum chemistry calculations.
The GPView provides full graphic user interface (GUI) which makes it very easy to use.
Amber Tools consists of several independently developed packages that work well by themselves, and with Amber itself.
The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models. Web MO is the most popular interface to computational chemistry programs, with over 22,000 unique Web MO licenses issued to date!
The Amber Tools suite is free of charge, and its components are mostly released under the GNU General Public License (GPL). Web MO has released a new Android app and updated its popular Apple i OS app! The Android and i OS Web MO apps provide equivalent features including: Thousands of students and scientists use the Web MO apps on their smartphones and tablets each month. More computational services are moving away from local hardware and into the "cloud".