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#
# ABF calculation
#
# 2KQT and Amt
#
##################################################
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##################################################
# MD SECTION
##################################################


binCoordinates Equilibration.restart.coor
binVelocities Equilibration.restart.vel
extendedSystem Equilibration.restart.xsc


# Harmonic constraints

constraints on
consref Minimization_restraints.pdb
conskfile Minimization_restraints.pdb
constraintScaling 2
consexp 2
conskcol B




# NUMBER OF MD-STEPS

numsteps             20000000


# TOPOLOGY

structure            Simulation_QwikMD.psf


# FORCE FIELD

paraTypeCharmm       on
parameters toppar_water_ions_namd.str
parameters toppar_all36_carb_glycopeptide.str
parameters par_all36_lipid.prm
parameters par_all36_na.prm
parameters par_all36_prot.prm
parameters par_all36_carb.prm
parameters par_all36_cgenff.prm
parameters AMT_qwikmd.str



# 1-4 TERMs

exclude              scaled1-4
1-4scaling           1.0


# INPUT FILES

coordinates          Simulation_QwikMD.pdb

#temperature          300.0


# OUTPUT FILES

binaryoutput         no  
binaryrestart        yes

outputname           abf_00_0
restartname          abf_00


# DCD FILE

dcdFile              abf_00.dcd


# FREQUENCY FOR DUMPING OUTPUT DATA

outputenergies       1000
outputtiming         1000
outputpressure       1000
restartfreq          1000 
XSTFreq              1000 
dcdFreq              1000


# CUT-OFFs

hgroupcutoff         2.8
switching            on
switchdist           10.0
cutoff               12.0
pairlistdist         14.0


# CONSTANT-T

langevin             on
langevintemp         300.0
langevindamping      1.0 


# MULTIPLE TIME-STEP PROPAGATOR

timestep             0.5


# SHAKE/RATTLE

rigidbonds           none


# PARALLELISM

stepspercycle        16
splitpatch           hydrogen
margin               2.0


# ABF SECTION

colvars              on
colvarsConfig        Distance.in