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Agilio Padua
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README.md

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@@ -58,13 +58,13 @@ How to build an initial configuration of a molecular or ionic system.
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[fftool](http://www.github.com/agiliopadua/fftool) page.
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2. Use the `fftool.py` script to create `.xyz` files for the molecules
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2. Use the `fftool` script to create `.xyz` files for the molecules
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in your system and an input file for
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[Packmol](http://www.ime.unicamp.br/~martinez/packmol/). For help
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type `fftool.py -h`. For example, to build a simulation box with 20
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type `fftool -h`. For example, to build a simulation box with 20
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ion pairs and a density of 3.0 mol/L do:
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fftool.py 20 c4c1im.zmat 20 ntf2.zmat --rho 3.0
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fftool 20 c4c1im.zmat 20 ntf2.zmat --rho 3.0
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3. Use Packmol with the `pack.inp` file just created to buid the
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simulation box (adjust the density if necessary):
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Atom coordinates will be written to a file `simbox.xyz`. You can
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use a molecular viewer such as VMD to look at the `.xyz` files.
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4. Use `fftool.py` to build the input files for LAMMPS or DL_POLY
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4. Use `fftool` to build the input files for LAMMPS or DL_POLY
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containing the force field and the coordinates:
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fftool.py 20 c4c1im.zmat 20 ntf2.zmat --lammps
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fftool 20 c4c1im.zmat 20 ntf2.zmat --lammps
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Information on the force field file format and on more geeral or
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advanced used is available at the

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