Software

 

You will be using Sire to perform the simulations in this practical. The sqm package, part of AmberTools14, will be used to perform the quantum mechanics. Both of these packages are free and available for a wide range of systems. You can download this software and continue this practical at home if you are unable to finish it today.


SIRE

If you don’t have a copy of Sire installed, please download a copy from here and follow the installation instructions on that page. By default, Sire will be installed into a “sire.app” directory in your home directory, with all Sire programs installed in “sire.app/bin”. To make things easier, please set the “SIRE” environment variable to point to the full path of the sire.app directory, e.g.

before continuing the practical, where “/install_directory” is the full path to the directory in which you installed “sire.app”. For example, if you have installed “sire.app” into your home directory, you can type;

$SIRE/bin/quantomm

export AMBERHOME=/install_directory/amber14

if you are using bash, and where “/install_directory” is the full path to the directory that contains “amber14”.


Once you have both Sire and AmberTools14 installed (and have set “AMBERHOME” to point to the amber14 installation directory) then please start the practical.

AMBERTOOLS

If you don’t have a copy of AmberTools14 installed, please download a copy from here and follow the installation instructions on that page. Once installed, please make sure that you set the “AMBERHOME” environment variable to point to the directory you installed the software, e.g. type;

export SIRE=$HOME/sire.app

export SIRE=/install_directory/sire.app

All of the Sire programs are installed in the $SIRE/bin directory. For example, please make sure that you can run the ‘quantomm’ program by typing;