Applying external force

# input

set toppar /p/home/kuangz/CharmmGUItoppar

set restart 1

set fixed 0

set temperature 308.15

set inputname min

set output heat

coordinates ../com.pdb

structure ../com.psf

if { $restart } {

binCoordinates $inputname.restart.coor

binVelocities $inputname.restart.vel ;# remove the “temperature” entry if you use this!

extendedSystem $inputname.restart.xsc

} else {

temperature $temperature; # initial temperature

cellBasisVector1 242 0 0

cellBasisVector2 0 242 0

cellBasisVector3 0 0 410

cellOrigin 0 0 0

}

paraTypeCharmm on

parameters $toppar/par_all36m_prot.prm

parameters $toppar/par_all36_cgenff.prm

parameters $toppar/toppar_all36_nano_lig.str

# output

outputname $output

binaryoutput no

outputEnergies 50000

restartfreq 50000

dcdfreq 50000

xstFreq 50000

wrapWater on

wrapAll on

dcdUnitCell yes

# mobile atom selection:

if { $fixed } {

fixedAtoms on

fixedAtomsFile fixed.pdb

fixedAtomsCol B

}

constraints on

consexp 2

consref fixed.pdb

conskfile fixed.pdb

conskcol O

# Basic dynamics

exclude scaled1-4

1-4scaling 1

# COMmotion yes # dielectric 1.0

# Simulation space partitioning

switching on

switchdist 10

cutoff 12

pairlistdist 16

# Multiple timestepping

firsttimestep 0

timestep 2.0

stepspercycle 20

pairlistsPerCycle 2

nonbondedFreq 2

fullElectFrequency 2

rigidbonds all #! SHAKE_H SPC

# Temperature control

# Langevin Dynamics

langevin on; # do langevin dynamics

langevinDamping 1;# damping coefficient (gamma) of 1/ps

#langevinTemp $temperature; # bath temperature

langevinHydrogen no; # don’t couple langevin bath to hydrogens

# Constant Pressure Control

langevinPiston on

langevinPistonTarget 1.01325 ;# in bar -> 1 atm

langevinPistonPeriod 100.

langevinPistonDecay 50.

# langevinPistonTemp $temperature

useFlexibleCell yes

useGroupPressure yes

useConstantRatio yes

# useConstantArea yes

margin 3

# PBC

PME yes

# the number of grid points should be a multiple of 2, 3, or 5

#PMEGridSizeX 182

#PMEGridSizeY 182

#PMEGridSizeZ 276

PMEInterpOrder 6

PMEGridSpacing 1.0

#extraBonds on

#extraBondsFile extra.psf

#colvars on

#colvarsConfig SGAU.in

#colvarsInput $inputname.restart.colvars.state

#

# Scripting

# minimize 10000

# run 100000000

#

# heating up

# reassignFreq 10000 # reassignTemp 0.0 # reassignIncr 30.0 # reassignHold $temperature # reinitvels $temperature # run 58500000

set temp 283.15

while { $temp < 308.15 } {

langevinTemp $temp

langevinPistonTemp $temp

run 1000

set temp [expr $temp + 5.0]

}

# set freq 59520

set totalStep 300000000

eFieldOn yes

for {set i 0} { $i < $totalStep } {incr i} {

if {$i % 2 == 0} {

eField 0.000002 0.0 0.0

} else {

eField -0.000002 0.0 0.0

}

run $freq

}