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MCCCS Towhee (forcefield)

 

 

Overview
    This section explains the forcefield utility program. This program is designed to translate the native units of many different forcefields into the Towhee units and then output a towhee_ff file with the current format.
Compiling
    Unlike most of the other utility programs, forcefield is compiled in the Source directory instead of the Utils directory because it shares several subroutines with towhee. Some of the subroutines in this utility program are very large and cause many common optimizers to overload memory. Therefore I strongly suggest that you turn off the optimizers when compiling this utility. The following direction work and assume you are starting in the base directory of the distribution.
      cd /towheebase
      ./configure FFLAGS=''
      cd Source
      make clean
      make forcefield
    This creates a forcefield executable that can then be run from the command line.
Features
    When you run this program from the command line it will prompt you to choose from a list of force field names to generate. Most of these commands simply translate the appropriate built in subroutine of data to output a force field file that should be identical to the one provided with the distribution. Here are some of the other options that do something other than just generate the specified force field file.
    • All: this command generates all of the force field files that are simple translations of the subroutines that are included in the main Towhee distribution. This command is useful for regenerating all of those forcefield files after making a change to the force field format.
    • CharmmFile: translates certain kinds of charmm force field files into a Towhee force field file.
    • PMF: this command translates a sequence of potential of mean force (PMF) files into a tabulated potential and outputs a towhee_ff_PMF file. For more information about generating PMF file please see the rdf2pmfpair utility.
    • Setfl: this command translates an Embedded Atom Method potential in the Setfl format into the Towhee format.
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Send comments to: Marcus G. Martin
Last updated: June 11, 2009