Lysozyme in water with SOMD

Antonia Mey School of Chemistry University of Edinburgh

This tutorial will cover how to prepare a pdb file using FESetup and then run a simple molecular dynamics simulation with SOMD. It will not cover how to install these programs. However, FESetup can be downloaded here and sire.app which includes the molecular dynamics simulation app SOMD, can be obtained here.

Some familiarity with a terminal, either Linux or OSX, will be assumed: e.g. creating directories and changing between directories. This tutorial is only suitable for working on a computer running either Linux or OSX.

Before you start the tutorial make sure that both FESetup and SOMD are correctly installed, i.e. typing FESetup -h in your terminal will give similar output to:

$: FESetup -h

=== FESetup SUI version: 0.6.4 ===

usage: dGprep.py [-h] [--tracebacklimit TRACEBACKLIMIT] [infile]

positional arguments:
infile                input file in INI format, if not given then just
                    output defaults

optional arguments:
-h, --help            show this help message and exit
--tracebacklimit TRACEBACKLIMIT
                    set the Python traceback limit
                    

For installation help on FEsetup, have a look at the FESetup installation page.

Next check that when typing somd results in something like:

usage: somd [-h] [-C [CONFIG]] [-H] [--author] [--version]
            [-t [TOPOLOGY_FILE]] [-c [COORDINATE_FILE]] [-d [DEVICE]]
            [-n [NMOVES]] [-p [PLATFORM]]

Perform molecular dynamics using OpenMM

optional arguments:
  -h, --help            show this help message and exit
  -C [CONFIG], --config [CONFIG]
                        Supply an optional CONFIG file to control the
                        calculation.
  -H, --help-config     Get additional help regarding all of the parameters
                        (and their default values) that can be set in the
                        optionally-supplied CONFIG file
  --author              Get information about the authors of this script.
  --version             Get version information about this script.
  -t [TOPOLOGY_FILE], --topology_file [TOPOLOGY_FILE]
                        The Amber topology file containing the system.
  -c [COORDINATE_FILE], --coordinate_file [COORDINATE_FILE]
                        The Amber coordinate file giving the coordinates of
                        all of the atoms in the passed topology file.
  -d [DEVICE], --device [DEVICE]
                        The device ID of the GPU on which you want to run the
                        simulation.
  -n [NMOVES], --nmoves [NMOVES]
                        The number of Molecular Dynamics moves you want to
                        run.
  -p [PLATFORM], --platform [PLATFORM]
                        The OpenMM platform on which you want to run the
                        simulation.

somd is built using Sire and OpenMM and is distributed under the GPL. For more
information please visit http://siremol.org

Please supply the name of an existing topology and coordinate file.
(cannot find coordinate file system.crd)
(cannot find topology file system.top)

If you have any trouble with this have a look at the installation page to get some help with installing the Sire molecular library which includes SOMD.

Start tutorial