###################################################
# Methane hydration
###################################################


# MD SETUP

timestep                1.0
numsteps                250000


# FLEXIBLE CELL

useflexiblecell         no


# INPUT

structure               ../solvate.psf 
parameters              ../../common/par_all22_prot.inp
paraTypeCharmm          on

coordinates             ../solvate.pdb
bincoordinates          ../thermalize.coor
binvelocities           ../thermalize.vel

# OUTPUT

outputenergies          100
outputtiming            100
outputpressure          100
binaryoutput            no

outputname              abf_window1_0
restartname             abf_window1

restartfreq             1000
binaryrestart           yes

XSTFreq                 100


# DCD TRAJECTORY

DCDfile                 abf_window1.dcd
DCDfreq                 1000


# PBC

cellbasisvector1        30.00  0.00   0.00 
cellbasisvector2         0.00 30.00   0.00 
cellbasisvector3         0.00  0.00  60.00


# PME

PME                     yes
PMETolerance            10e-6
PMEInterpOrder          4

PMEGridSpacing          1.0


# WRAP WATER FOR OUTPUT

wrapWater               off


# CONSTANT-T

langevin                on
langevinTemp            300.0
langevinDamping         1.0


# CONSTANT-P
# This is a constant-V simulation

LangevinPiston          off


# SPACE PARTITIONING

splitpatch              hydrogen
hgroupcutoff            2.8
stepspercycle           20
margin                  1.0


# CUT-OFFS

switching               on
switchdist               9.0
cutoff                  11.0
pairlistdist            13.0


# RESPA 

fullElectFrequency      4
nonbondedFreq           2


# 1-4 NON-BONDED

exclude                 scaled1-4
1-4scaling              1.0


# COM

commotion               no
zeroMomentum            yes


# SHAKE

rigidbonds              all 


# ABF SECTION

colvars              on
colvarsConfig        Transport-window1.in