Getting started

Welcome to the Iphigenie molecular dynamics (MD) simulation program.
To get started follow these steps:

1. Download the latest version of Iphigenie

Each version subdirectory contains tar'ed and gzip'ed files that can be expanded.

:::bash
tar -xzpvf <filename>

from a common root directory.
The 'program' and 'share' files are obligatory. The 'examples' are useful to get an idea what features Iphigenie provides and how they are operated. The last file 'testsuite' is mainly intended for developers and provides reference output for different setups to check if everything runs correctly.

iphigenie-XXX-program.tar.gz   :   the source code and build system
iphigenie-XXX-share.tar.gz     :   parameter and data files
iphigenie-XXX-examples.tar.gz  :   input file examples
iphigenie-XXX-testsuite.tar.gz :   reference input and output

2. Compile Iphigenie

Follow the compiling instructions. If in doubt about the validity of your build, run the Test Suite to verify the numerics of your executable.

3. Set up the Simulation System

The input files for the MD executable iffi have to be generated from protein data base (.pdb) files and protein structure files (.psf) analogous to CHARMM and NAMD. You can built these files, for example, with tools provided by the visual molecular dynamics (VMD) package. Convert these files to the native iffi input format by the xpl2lis tool.

4. Prepare your Control File

The control file ctl.xml contains the full set of input options (follow this link for details) and comments. You will only need a small subset of tags for a typical task. For inputs of such tasks see the examples.

5. Run the Simulation

Use the iffi executable to run your simulation.