MPI Dock Demo

The demo is an example for how to use dock with MPI (Message Passing Interface). This is the standard protocol for parallel communication between nodes in a cluster. In order to run the demo, MPI needs to be installed. The latest version of MPI can be obtained from http://www-unix.mcs.anl.gov/mpi/

Prior to running the demo, set MPICH_HOME to your MPI installation e.g. /opt/mpich-1.2.7

The contents of the current directory are

script_demo             This script executes dock. It needs to be edited to set the install 
			directories for DOCK, MPI and the list of available nodes. The script 
			assumes that a default machine file exists. In case you are using 
			MPICH2, run mpdboot to initialize nodes first. 
			e.g. "mpdboot -v -n 16 -r ssh -f .mpd.hosts" 

script_clean            This script cleans up (removes) the various files
                        generated during the demonstration

1_struc/                This directory contains receptor and ligand coordinate files.
                        Three small ZINC libraries kindly provided by the Shoichet Laboratory 
                        (http://blaster.docking.org/zinc) are included for testing purposes.
			   zinc_nci_0010.mol2         (contains    9 molecules + ligand from crystal )
			   zinc_nci_0500.mol2         (contains  500 molecules)
			   zinc_nci_1000.mol2         (contains 1000 molecules)
			   1VRT.lig.1000copies.mol2   (contains 1000 copies of ligand from crystal to evaluate mpi timings)

2_site/                 This directory contains sphere generation files.

3_grid/                 This directory contains grid generation files.

4_dock/                 This directory contains docking files.
			Note that "mpi.in" specifies which library will be docked.
			The library is set to zinc_nci_0010.mol2 (default)
