An Amino Acid Ionic Liquids (AAILs) Supplement for the Original CL&P and CL&Pol

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Description

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This repository contains the nonpolarizable and polarizable force field parameters and files for amino acid ionic liquids (AAILs), which are compatible with the CL&P, CL&Pol, and fftool. Most parameter files and scripts in this repository are similar to those in CL&P and CL&Pol, except for pol_param/modified_lj.data and scripts/modifyLJ, which are used to modify the Lennard-Jones sigma parameters to mitigate the overestimated electrostatic acctraction between the bare hydrogens/small ions and negatively charged atoms.

If you use these parameters, please cite the following papers:

[my citation]

Usage of the new script modifyLJ

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The pol_param/modified_lj.data file contains atom type pairs whose the Lennard-Jones interaction's sigma parameter needs to be modified. The scripts/modifyLJ script is used to modify the Lennard-Jones sigma parameters according to the modified_lj.data file. The script will read the pair-sc.lmp file (the polarizable LAMMPS pair potential files, which each line contains the LJ parameters for each atom type pair and comments indicating their atom type names)

• usage: modifyLJ [-ip INPUTPAIRFILENAME] [-op OUTPUTPAIRFILENAME] [-lj MODIFIEDLJFILENAME]

• options:

  • -ip INPUTPAIRFILENAME: the input LAMMPS pair potential file, default is pair-sc.lmp
  • -op OUTPUTPAIRFILENAME: the output LAMMPS pair potential file, default is pair-sc-m.lmp
  • -lj MODIFIEDLJFILENAME: the modified Lennard-Jones sigma parameters file, default is pol_param/modified_lj.data

How to use

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To build nonpolarizable and polarizable LAMMPS inputs for AAILs using this supplement, please follow the following steps: (use [Cho][Ala] as an example, assume that Packmol has been installed)

1. copy all structure files (here, cholinium.zmat and ala.zmat), force field files (des.ff and ala.ff), and fftool script, into the working folder.

2. use fftool script to generate the Packmol input file for the system with 100 cholinium and 100 alanine molecules within the box with length of 35 Angstroms:

   fftool 100 cholinium.zmat 100 ala.zmat -b 35

3. use Packmol to generate the initial configuration:

   packmol < pack.inp

4. use fftool to build the input files for LAMMPS containing the force field and the coordinates, use -l to indicate LAMMPS format, and -a to indicate to write all I-J pairs, instead of only I-I pairs; this step will generate data.lmp and pair.lmp for further polarizable force field generation usage:

   fftool 100 cholinium.zmat 100 ala.zmat -b 35 -l -a

5. to further generate the polarizable system, copy polarizer, scaleLJ, coul_tt, modifyLJ scripts, and alpha.ff, fragment.ff, modified_lj.data files into current working folder.

6. use polarizer to generate the polarizable LAMMPS data file:

   polarizer -f alpha.ff data.lmp data-p.lmp

7. use scaleLJ to scale the Lennard-Jones sigma parameters according to the SAPT calculation, use -q option to make sure we are using the SAPT values instead of the predicted values. fragment.inp is a input file that identifies the atomic types corresponding to each fragment, here are ch and ala two fragments:

   scaleLJ -f fragment.ff -a alpha.ff -i fragment.inp -ip pair.lmp -op pair-scq.lmp -q

8. use coul_tt to add TT damping between dipoles and bare hydrogens/small ions, in this case, the atom types of bare hydrogens are 8 and 10, and the default TT damping factor $b_{tt}=4.5$ is used:

   coul_tt -d data-p.lmp -a 8 10 --btt 4.5

9. lastly, use modifyLJ to modify the Lennard-Jones sigma parameters:

   modifyLJ -ip pair-scq.lmp -op pair-scq-m.lmp -lj modified_lj.data