MBG wiki: heating-up NAMD script for T40Y

# To run this script type: namd2 <filename>
# modified
# Based on the NAMD-VMD online tutorial
# 

# input files
structure 		ionized.psf
coordinates 		ionized.pdb

parameters      	parallh22x.pro
parameters      	water+ions.par


#output files
outputname		output/heat_out
binaryoutput		off
restartname             output/restart
restartfreq             1000	# generation of restart files every 
				# 1000 x timestep fs
binaryrestart           yes
dcdFile			output/heat_out.dcd
dcdFreq			200 # writting dcd every 200 x timesteps fs

outputEnergies		20
outputTiming		200
xstFreq			200


#time and multiple-timesteps parameters 
#numsteps		1.0
timestep		2.0	#femto-seconds (fs)
stepsPerCycle		8

nonBondedFreq		2 #it means 2 x timestep
fullElectFrequency 	4 #it means 4 x timestep


#simulation space partitioning
switching		on
switchDist		10
cutoff			12
pairlistdist		13.5


#basic dynamics
temperature		0	#initial temperature for the system in Kelvin
COMmotion		no
dielectric		1.0
exclude			scaled1-4
1-4scaling		1.0
rigidbonds      	all

# Particle Mesh Ewald parameters:
# a full electrostatics method for use with
# periodic boundary conditions
Pme             	on
PmeGridsizeX    	128 #grid for fft
PmeGridsizeY    	80  #grid for fft	
PmeGridsizeZ    	64  #grid for fft    


wrapWater       	on
wrapNearest		on

cellBasisVector1       125.49   00.00   00.00
cellBasisVector2        00.00   77.64   00.00
cellBasisVector3        00.00   00.00   65.03
cellOrigin              -0.79   -4.00   -0.38

fixedAtoms		on
fixedAtomsForces	on
fixedAtomsFile		fix_backbone.pdb
fixedAtomsCol		B

constraints		on
consRef			restrain_ca.pdb
consKFile		restrain_ca.pdb
consKCol		B

langevin		on
langevinDamping		10
langevinTemp		320
langevinHydrogen	on

langevinPiston		on
langevinPistonTarget	1.01325
langevinPistonPeriod	200
langevinPistonDecay	100
langevinPistonTemp	320

useGroupPressure	yes


# THE PROTOCOL TO BE RUN

# run one step to get into scripting mode
minimize 0

# turn off until later
langevinPiston  off

# minimize nonbackbone atoms
minimize 2000
output output/min_fix

# min all atoms
fixedAtoms      off
minimize 2000
output output/min_all

# heat with CAs restrained
# langevin      on
run 6000
output output/heat_ca

# equilibrate volume with CAs restrained
langevinPiston  on
run 10000
output output/equil_ca

# equilibrate volume without restraints
constraintScaling       0
run 100000