SourceForge.net Logo
MCCCS Towhee (Utility Summary)

 

 

Overview
    This section summarizes the utility programs that are included with the Towhee code distribution (generally in the Utils directory). It also contains links to detailed information explaining how to use each of these programs.
Post-Processing Data Analysis Utilities
    analyse_histogram
      This program is designed for use in conjunction with the towhee_histogram files and is used to analyze the histogram data generated by the grand canonical ensemble.
    analyse_movie
      This program is designed for use in conjunction with the Towhee MCCCS file and is used to compute quantities from the towhee_movie file.
    fitcoex
      This program replaces the old fitvlcc utility and is designed for use in conjunction with the towhee_vlcc output files in order to compute the critical temperature and critical density from a sequence of single-component vapour-liquid simulations.
    parse_vlcc_plots
      This script is designed for use in conjunction with the standard towhee output file used in a single-component vapour-liquid simulation and it extracts the snapshot and block average information from that file in order to create a series of plottable files.
Pre-Processing File Conversion Utilities
    charmm2pdb
      This program is designed to translate the polypeptide pdb files generated by Charmm into the standard pdb format to allow further processing via the pdb2towhee routine.
    faux2towhee
      This program is designed to translate some zeolite coordinate files that were kindly provided to me by David Faux into a format suitable for Towhee. This utility is unlikely to be of use to anyone else, but may serve as an example for other one-time file translations.
    forcefield
      This program uses many of the main Towhee subroutines along with several additional subroutines to convert a forcefield from a different format into the Towhee Force Field Format. It is capable of generating almost all of the force field files included in the ForceFields directory of the Towhee distribution.
    pdb2towhee
      This program is designed to translate the standard pdb files into appropriate Towhee files for starting a simulation. In all cases it will output a towhee_coords file full of the system coordinates. In certain cases it will output a towhee_altinp file with partial information required to set up a polypeptide molecule template.
    rdf2pmfpair
      This program converts a radial distribution function into a potential of mean force. The potential of mean force file is then suitable for conversion into a tabulated pair potential using the forcefield program.
    unitcell
      This program is used to take a towhee_coords file and duplicate it any number of times in the x, y, and z dimensions in order to perform a larger simulation.
    xmd2towhee
      This program converts EAM force field files that are in the XMD format into a format suitable for use in Towhee.
    xyz2towhee
      This program converts simple xyz format files into a series of files that can be used to construct a towhee_coords file for Towhee.

 

Return to the main towhee web page


Send comments to: Marcus G. Martin

Last updated: December 14, 2006