APPENDIX B: Minimization Step for [Bmim][PF₆]

Keyword

Value/Name

Comment

#Input Topology and Initial Structure

Structure

BMIMPF₆.psf

#Reading the topology file

Coordinates

BMIMPF₆.pdb

#Coordinate File

# Force field Block

paratypecharmm

on

#Selecting the type of force field (CHARMM)

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

PME on

on

Use Particle-Mesh Ewald (PME)summation for long- range electrostatics

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

minimization

on

#Do a conjugate gradient minimization

#Output Block

outputenergies

100

#Interval in integration steps of writing energies

outputtiming

100

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

outputname

BmimPF₆_min

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

restartname

BmimPF₆_restart

#Filename holding the restart name for holding velocities and coordinates

restartfreq

100

#Interval between writing out the restart      
coordinates and velocities      

DCDfile

BmimPF₆_min

# Trajectory filename (binary file)

dcdfreq

100

#Frequency of writing structural snapshots to trajectory file

numsteps

100000

#Number of steps for minimization

# 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