Mod:Hunt Research Group/ilff

install

the Agilio Padua git hub ilff link
read the README.md file
fftool is a python script by Agilio that builds a simulation box and the corresponding force field for systems containing molecules, ions or extended materials using Packmol, the output files are in a format suitable for the LAMMPS, DL_POLY or Gromacs
cd to your the directory you are building your MD box

git clone https://github.com/agiliopadua/ilff.git
git clone https://github.com/agiliopadua/fftool.git

you will find a new directories called fftool and ilff

use

lets build a box for BmimNtf2 256 ion pairs

first create an input file for packmol, pack.inp

you will need the density in mol/L

check the pressure and temperature

room temp 25 C=293.15 K (you probably want higher than this)

standard pressure =1 atm=101 kPa

if the density is in kg/m^3 you will need to convert

either calculate or use an IL supplier site to calculate the molecular mass (this is the molar mass ie 1mol id x g)

1m^3=1000L

x kg/m3=x000g/1000L=x g/L=(x/MR) mol/L

for example

MR=419.36 g/mol

density 1.42g/cm3 at 20 C

temp=303.15 ie 30 C

pressure=100kPa ie 1atm

density=1432kg/m^3 =1432/419mol/L=3.4mol/L

copy the files you need into the directory you want to run the MD

cp ilff/c4c1im.zmat .
cp ilff/ntf2.zmat .
cp ilff .

the fftool command is

fftool/fftool 256 c4c1im.zmat 256 ntf2.zmat -r 3.40

where -r is rho the density

and you will see in the terminal

density 3.400 mol/L  volume 250063.5 A^3
molecule descriptions
  c4c1im.zmat
  ntf2.zmat
species                 nmol  bonds   charge
  c4c1im+                256  none   +1.0000
  tf2N-                  256  none   -1.0000
packmol file
  pack.inp

it is also possible to supply the dimension of one side of a cubic box in angstrom

fftool 40 ethanol.zmat 300 spce.zmat -b 20.0