Workflow Tutorial

Welcome to the first tutorial of eSBMTools.

In this tutorial, we will set up a basic workflow of a simple simulation
using the 2ICT protein

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→ To start the example, type in the following command in the terminal:

                $> python workflow.py (sourceforge.net)

→ This command will run the python script in the folder and prepare the
necessary files for the MD simulation. The files that are generated are:

            -2ICT.gro
            -2ICT.top
            -md.mdp
            -table.xvg
            -log.file

NOTE This example uses the C-alpha level of graining.

→ Now run the GROMACS preprocessor with the following command:

    $> grompp -f md.mdp -c 2ICT.gro -p 2ICT.top

This will generate the corresponding mdout.mdp and the topol.tpr files.

→ Finally we run the simulation with the mdrun command as follows:

    $> mdrun -c 2ICT.gro -tablep table.xvg

selecting the C-alpha options when prompted. This then outputs 4 files:

            -ener.edr
            -state.cpt
            -traj.trr
            -traj.xtc

→ The trajectory when rendered in PyMol will look like this (with some extra visual changes of course!):

******************************************************************************** For an explanation of the functions used in this example, read the Functions wiki. Cheers!