MBG wiki: heating-up NAMD script

# 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
# paraTypeCharmm                on

#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/equi_out.dcd
dcdFreq                 200 # writting dcd every 200 x timesteps fs

#imdon          yes
#imdfreq                1
#imdport                3111


outputEnergies          10
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       130.30   00.00   00.00
cellBasisVector2        00.00   76.01   00.00
cellBasisVector3        00.00   00.00   63.87
cellOrigin              -0.70   -4.34   00.06

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