APPENDIX E: Production Step for [Bmim][PF₆]

Keyword

Value/Name

Comment

#Input Topology and Initial Structure

Structure

BMIMPF₆.psf

#Reading the topology file

Coordinates

bmimPF₆_equil.coor

#Coordinate File from the equilibriation step

# Force field Block

paratypecharmm

on

#Selecting the type of force field

parameters

BMIMPF₆.params

#The forcefield parameter file

exclude

scaled 1-4

#Specifies which pairs of bonded atoms should be excluded from non-bonded interactions.

dielectric

1.0

#Value of 1 indicates no modification of the electrostatic interactions

# Long Range Interactions

switching

on

#Switch on the Electrostatic and vdW interaction and divide it into the local and non-local terms

switchdist

18

# Distance at which the switching function is first applied

cutoff

18.5

#Local interaction distance being common to both Electrostatic and vdW interaction

pairlistdist

20

#Distance between pair of atoms so as to be included in the pairlists

margin

0

#Extra Distance used in selecting the patches

stepspercycle

20

#Frequency for updating the list of atoms as described by pairlistdist

rigid bonds

all

#Applying SHAKE algorithm to all covalently bonded C-H bonds

rigidTolerance

0.0001

# Desired accuracy in maintaining SHAKE ed bond lengths

rigidIterations

500

#Maximum Number of SHAKE iterations

#Ewald Electrostatics(Long Range Electrostatics)

PME on

on

Use Particle-Mesh Ewald (PME)summation

PMEGridSizeX

32

#Setting the grid of points for fast calculation of reciprocal terms in X,Y, and Z direction

PMEGridSizeY

32

PMEGridSizeZ

32

PMETolerance

0.000001

# Block Specifying the Parameters for Integrator and MTS (Multiple Time Step)

timestep

1

Time step for integration i.e 1 fs

fullElectFrequency

4

# The interval between calculation of long- range electrostatics using PME method.

#Output Block

outputenergies

100

#Interval in integration steps of writing energies

outputtiming

100

# Interval of writing timing (basically, speed, "memory allocation, etc)

outputname

bmimPF₆_NPT

#File name where the final coordinates and velocities are stored in *.coor and *.vel  extension

restartname

bmimPF₆_NPT_r

#Filename holding the restart name for holding velocities and coordinates

restartfreq

100

#Interval between writing out the restart            
coordinates and velocities      

DCDfile

bmimPF₆_NPT

# Trajectory filename (binary file)

dcdfreq

100

#Frequency of writing structural snapshots to trajectory file

#Molecular Dynamics Block

seed

1010

# Random Number seed to generate initial Maxwell distribution of velocities

numsteps

1000000

# Number of Integration Steps

temperature

300

#  Temperature for initial velocity distribution

#Pressure Control (Nose Hoover Langevin)

LangevinPiston

on

#Whether use Langevin Piston

LangevinPistonTarget

0.98

# The constant value of Pressure required in bar

LangevinPistonPeriod

200

#barostat oscillation time scale for Langevin piston method.(fs)

LangevinPistonDecay

100

#barostat damping time scale for Langevin piston method

LangevinPistonTemp

          300

#Specifies barostat noise temperature for Langevin piston method

# Temperature Control

langevin                     

on

#whether or not Langevin dynamics active.

langevinTemp

298

#Temperature to which atoms affected by Langevin dynamics will be adjusted.

langevinDamping

5

#Langevin coupling coefficient to be applied to all atoms fs-1

# Periodic Boundary Conditions

cellBasisVector1

40

0

0

#Dimension of the Box in x direction in Å

cellBasisVector2

0

40

0

#Dimension of the Box in y direction in Å

cellBasisVector3

0

0

40

#Dimension of the Box in z direction in Å

cellOrigin

20

20

20

# Centre of the Cell in Å