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agiliopadua committed Jun 11, 2015
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Expand Up @@ -58,13 +58,13 @@ How to build an initial configuration of a molecular or ionic system.
[fftool](https://www.github.com/agiliopadua/fftool) page.


2. Use the `fftool.py` script to create `.xyz` files for the molecules
2. Use the `fftool` script to create `.xyz` files for the molecules
in your system and an input file for
[Packmol](https://www.ime.unicamp.br/~martinez/packmol/). For help
type `fftool.py -h`. For example, to build a simulation box with 20
type `fftool -h`. For example, to build a simulation box with 20
ion pairs and a density of 3.0 mol/L do:

fftool.py 20 c4c1im.zmat 20 ntf2.zmat --rho 3.0
fftool 20 c4c1im.zmat 20 ntf2.zmat --rho 3.0

3. Use Packmol with the `pack.inp` file just created to buid the
simulation box (adjust the density if necessary):
Expand All @@ -74,10 +74,10 @@ How to build an initial configuration of a molecular or ionic system.
Atom coordinates will be written to a file `simbox.xyz`. You can
use a molecular viewer such as VMD to look at the `.xyz` files.

4. Use `fftool.py` to build the input files for LAMMPS or DL_POLY
4. Use `fftool` to build the input files for LAMMPS or DL_POLY
containing the force field and the coordinates:

fftool.py 20 c4c1im.zmat 20 ntf2.zmat --lammps
fftool 20 c4c1im.zmat 20 ntf2.zmat --lammps

Information on the force field file format and on more geeral or
advanced used is available at the
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