ions.lt
fadc25d704efmaster

ions.lt
View Options

			# We define two molecule classes to represent Na+ and Cl- ions, respectively.
			# This may seem like overkill since they both only consist of one atom each.


			# Note: Monovalent ion parameters for Ewald and SPC/E water
			# are from: Joung & Cheatham JPCB (2008)
			# These Lennard Jones parameters match the parameters for ions
			# in SPC/E water in the "frcmod.ionsjc_spce" file distributed
			# with Amber (the 2010 version).


			NaIon {
			write_once("In Settings") {
			pair_coeff @atom:Na @atom:Na lj/charmm/coul/long 0.3526418 1.212
			}

			write_once("Data Masses") {
			@atom:Na 22.9898
			}

			# assumes "full" atom style
			write("Data Atoms") {
			$atom:Na $mol @atom:Na 1.0 0.00000 0.00000 0.000000
			}
			} # NaIon


			ClIon {
			write_once("In Settings") {
			pair_coeff @atom:Cl @atom:Cl lj/charmm/coul/long 0.0127850 2.711
			}

			write_once("Data Masses") {
			@atom:Cl 35.453
			}

			# assumes "full" atom style
			write("Data Atoms") {
			$atom:Cl $mol @atom:Cl -1.0 0.00000 0.00000 0.000000
			}
			} # ClIon


			write_once("In Init") {
			# -- Default styles for ions --
			units real
			atom_style full
			# (Hybrid force fields were not necessary but are used for portability.)
			pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0
			kspace_style pppm 0.0001
			pair_modify mix arithmetic
			}

			# Optional: Define a group named "ions" consisting of either Na or Cl ions.
			write_once("In Settings") {
			group ionNa type @atom:NaIon/Na @atom:NaIon/Na
			group ionCl type @atom:ClIon/Cl @atom:ClIon/Cl
			group ions type @atom:NaIon/Na @atom:ClIon/Cl
			}