Ionize is a threaded program for placing counterions near a biological molecule in preparation for molecular dynamics simulations. In this case, placement is performed by calculating the coulombic potential due to the molecule in the nearby volume, and placing ions at points of minimal energy. After each ion is placed, the potential is updated, so that subsequent ions will be placed in response to this. Unlike some ion placement tools, ionize should be used prior to solvation so that the potential from unequilibrated water does not interfere with it (the addition of water would also make the energy calculations even more time consuming). Ionize is designed to be used on multiple processors; it uses a pthreads parallel implementation to run on shared memory machines (any traditional multiprocessor machine, or shared memory clusters such as an SGI Altix). After ionize is finished, you should solvate your system normally.
The ionize distribution comes with a makefile
for a variety of supported target architectures. Type make with
no arguments to see a list of possible targets, and make TARGET
to build ionize for the architecture TARGET. Ionize is written
in standard C; current compilation options exist for gcc and icc.
Ionize requires as input a pdb file of the molecule to have ions added with the charge of each atom in its beta field, and will output a pdb containing the ion coordinates. Running the ionize executable with no arguments will bring up a short list of possible options, which is reproduced below:
ionize: Place ions by finding minima in a coulombic potential
Usage: ionize (options) input.pdb output.pdb
input.pdb must be a pdb file with atom charges in the beta field
Optional arguments (with defaults):
-n number of ions to place (1)
-r Minimum distance from ions
to solute (6.0)
-i Minimum distance between placed ions (10.0)
-g Grid spacing in angstroms (0.5)
-b Additional perimeter to search for ion locations (10.0)
-t ion name (SOD)
-q ion charge (1.0)
-p max_processors (1)
Most of these options should be fairly self-explanatory. Note that ionize currently only adds one ion type at a time; future versions will support both addition of multiple ion types, and saving of the energy grid for later use. Note that the -p switch specifies the maximum number of processors to be used by ionize, but it will not try to exceed the maximum number available (for example, the number allocated on an Altix run).
Ionize can also be run from a configuration file, using the wrapper script runionize. In this case, ionize is run with the command
runionize configfile
where configfile contains options formatted as for a
SODIUM
input file.
Ionize and the associated infrastructure were written by Peter Freddolino, John Stone, and Leonardo Trabuco. Please contact Peter Freddolino with any questions or comments.
Ionize is released under the UIUC Open Source License. This license is reproduced in the file LICENSE included with the ionize source distribution.
You can test your ionize installation by running make test in the ionize build directory. This will run a short ionize job on a small alpha helix and compare the results to a standard answer included in the ionize distribution. The differences, if any, will then be displayed. You should be worried if there are any differences outside of the last significant digit of the coordinates.