Setting up Relative Alchemical Free Energy Simulations with FESetup

Software requirements

FESetup and its tutorials can be downloaded from http://ccpforge.cse.rl.ac.uk/gf/project/ccpbiosim/frs/

The release contains all basic tools (AMBERTools) and toolkits and should run out-of-the-box. If you wish to use your favourite MD package (Gromacs, AMBER/pmemd, CHARMM, NAMD) you can install these separately according to their installation instructions.

Detailled installation instructions can be found on the FESetup Wiki http://ccpforge.cse.rl.ac.uk/gf/project/ccpbiosim/wiki/?pagename=Installation

The installer will ask for a few basic questions before and after extraction and by default will install in the current directory. Invoking the installer with --help will show advanced installation options.

We will also need to update FESetup's source code to the latest development branch as outlined on the Wiki http://ccpforge.cse.rl.ac.uk/gf/project/ccpbiosim/wiki/?pagename=Installation

Basically:

> cd $FES_HOME/FESetupMM/lib/python2.7/site-packages/
> mv FESetup FESetup.old
> svn co --username anonymous http://ccpforge.cse.rl.ac.uk/svn/ccpbiosim/FESetup/trunk FESetup

$FES_HOME is the top directory where you have installed FESetup.

A VirtualBox VM image has been prepared for those who do not run Linux natively (should also work for VMWare Player):

** The 32 bit version for both 32bit and 64bit host OSs: http://www.hecbiosim.ac.uk/tmp/hannes/FESetup32.ova (md5: 30f6ff6e591bc4d4c4c192d74fdf168e)

user: user
passwd: fesetup

Virtualbox: File->Import Appliance.... Change the shared folder in Settings->Shared Folder to a convenient location on the host system. In the VM the directory is called shared in your $HOME and should be called shared on the host too. The alias fesetup can be used to execute FESetup.

How to use FESetup

Details can be found in the Wiki including a manual and the tutorials. http://ccpforge.cse.rl.ac.uk/gf/project/ccpbiosim/wiki/

Please download the First Impressions and the T4 lysozyme tutorials because we will need them at the workshop.

http://ccpforge.cse.rl.ac.uk/gf/project/ccpbiosim/wiki/?pagename=Tutorials

Test the installation with the First Impressions tutorial.

Tutorials

The tutorial material can be found here http://www.hecbiosim.ac.uk/tmp/hannes/tutorials/

The API documentation is here http://www.hecbiosim.ac.uk/tmp/hannes/