LINKS TO INSTALL PROGRAMS TO BE USED IN THE WORKSHOPS
• GROMACS: https://manual.gromacs.org/current/install-guide/index.html
On the Linux operating system, you can install the Gromacs program from the terminal using the following commands:
Commands for the Linux distribution (Ubuntu)
sudo apt-get update
sudo apt-get install gromacs
Commands for Linux distribution (Fedora)
sudo dnf update
sudo dnf install gromacs
Commands for IOS distribution (Mac)
sudo port install gromacs
• NAMD: https://roshanbiophysics.wordpress.com/2017/04/21/installation-of-vmdand-namd-in-ubuntu/
• DL_POLY: https://dl-sdg.github.io/RESOURCES/dl_poly_instructions.html#
• LAMMPS: https://docs.lammps.org/Install.html
On Linux operating system, you can install the LAMMPS program from the terminal using the following commands:
Commands for the Linux distribution (Ubuntu)
sudo apt-get update
sudo apt-get install lammps
Commands for Linux distribution (Fedora)
sudo dnf update
sudo dnf install lammps
• NWChem: https://howtoinstall.co/en/nwchem
On Linux operating system, the NWChem program can be installed from the terminal using the following commands:
Commands for the Linux distribution (Ubuntu)
sudo apt-get update
sudo apt-get install nwchem
Commands for Linux distribution (Fedora)
sudo dnf update
sudo dnf install nwchem
• Orca: https://installati.one/install-orca-ubuntu-20-04/
On Linux operating system, you can install the ORCA program from the terminal using the following commands:
Commands for the Linux distribution (Ubuntu)
sudo apt-get update
sudo apt-get install orca
Commands for Linux distribution (Fedora)
sudo dnf update
sudo dnf install orca
• OVITO: https://www.ovito.org/windows-downloads/
On the page you will find the versions for Windows, IOS and Linux along with the installation manuals for the program.
• AMBER: https://ambermd.org/GetAmber.php#ambertools (When installing ambertools, the old DM engine known as Sander will be installed, which is the one that we will be using)
• HooMD: It is very easy and quick to install, it will be done together with the instructor in the first minutes of the session.
• OpenMM: http://docs.openmm.org/7.0.0/userguide/application.html
• Molden: https://snapcraft.io/install/molden/ubuntu
• VMD: https://bioinformaticsreview.com/20220301/how-to-install-vmd-on-ubuntu/
• Xmgrace: https://plasma-gate.weizmann.ac.il/Grace/
In Linux operating system, you can install the GRACE program from the terminal using the following commands:
Commands for the Linux distribution (Ubuntu)
sudo apt-get update
sudo apt-get install grace
Commands for the Linux distribution (Fedora)
sudo dnf update
sudo dnf install grace
