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min_equil.conf
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#############################################################
## JOB DESCRIPTION ##
#############################################################
# Minimization and Equilibration of
# Ubiquitin in a Water Sphere
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure ../input/1kx5_ready.psf
coordinates ../input/1kx5_ready.pdb
set temperature 310
set outputname ../output/min_eq
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters ../input/par_all36_prot.prm
parameters ../input/par_all36_na.prm
#this should be read last
parameters ../input/par_water_ions_36.prm
temperature $temperature
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 14.0
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 2.5 ;# damping coefficient (gamma) of 1/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# DX:
# 166.072998046875
# DY:
# 201.71700286865234
# DZ:
# 115.76899719238281
# Center:
# 7.356237411499023 23.249160766601563 0.38390639424324036
# Periodic Boundary Conditions
cellBasisVector1 166.1 0. 0.0
cellBasisVector2 0.0 201.8 0.0
cellBasisVector3 0.0 0 115.8
cellOrigin 0.0 0.0 0.0
wrapAll off
wrapWater on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSpacing 1.0
#manual grid definition
#PMEGridSizeX 45
#PMEGridSizeY 45
#PMEGridSizeZ 48
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 200.0
langevinPistonDecay 100.0
langevinPistonTemp $temperature
# Output
outputName $outputname
restartfreq 10000 ;# 500steps = every 20ps
dcdfreq 10000
xstFreq 10000
outputEnergies 1000
outputPressure 1000
#############################################################
## EXTRA PARAMETERS ##
#############################################################
fixedAtoms on
fixedAtomsForces on
fixedAtomsCol B
#The coordinate file will be used by default
constraints on
consref ../input/1kx5_ready.pdb
conskfile ../input/1kx5_cons.pdb
conskcol B
constraintScaling 1.0
#############################################################
## colvars ##
#############################################################
#colvars on
#colvarsConfig end_glue.cfg
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 1000
fixedAtoms off
minimize 10000
reinitvels $temperature
run 200000 ;# 400ps
constraintScaling 0.5
run 100000 ;# 200ps
constraintScaling 0.1
run 100000 ;# 200ps
constraintScaling 0.0
run 100000 ;# 200ps