Getting Started

Since mbtools is provided as part of the espresso molecular dynamics simulation package you will need to download and install Espresso before you can use it. Espresso can be downloaded free from http://espressomd.org.

Once you have installed espresso you can find mbtools by looking inside the packages subdirectory. Inside the packages/mbtools directory you will see a directory for each of the mbtools subpackages as well as an examples directory. All of the examples scripts should work out of the box except those involving colloids which require you to install icover.sh (see documentation for hollowsphere molecule type). To run the simplebilayer example cd to the examples directory and then type:


	$ESPRESSO_SOURCE/$PLATFORM/Espresso scripts/main.tcl simplebilayer.tcl
    
The first part of this command is simply the full path to the appropriate espresso executable on your machine. Obviously you will need to have the $ESPRESSO_SOURCE and $PLATFORM environment variables set for it to work. After this executable the relative paths to two tcl scripts are given. The first of these main.tcl is given as an argument to espresso and is therefore interpreted first by the espresso tcl interpreter. The second tcl script simplebilayer.tcl is in turn passed as an argument to main.tcl.

Why separate the tcl commands into two files ?

This is really a matter of preference but if we keep all of the key commands and complex coding in a single file main.tcl and delegate simple parameter setting to a separate file it tends to be much easier to manage large numbers of jobs with regularly changing requirements. Regardless of your personal preferences, the important point to note is that all of the important commands are contained in main.tcl and you should probably start there to get an understanding for how mbtools works.

Running the simplebilayer example should produce a directory called simplebilayer which contains the output from your simulation. To view the results cd to the simplebilayer directory and look at the contents. The directory contains many files including;

To visualise your results using the vmd scripts you need to make sure that you have vmd installed properly and that you have the special vmd procedures used by the espresso team (ie support for the loadseries command). Then you can visualise by typing;


      vmd -e vmd_animation.script