MBG wiki: NAMD minimisation and heating-up script

#
# Input files
#
structure               ionized.psf
coordinates             ionized.pdb
parameters              par_all27_prot_na.inp
paraTypeCharmm          on

#
# Output files & writing frequency for DCD
# and restart files
#
outputname              output/heat_out
binaryoutput            off
restartname             output/restart
restartfreq             1000
binaryrestart           yes
dcdFile                 output/heat_out.dcd
dcdFreq                 200

#
# Frequencies for logs and the xst file
#
outputEnergies          20
outputTiming            200
xstFreq                 200

#
# Timestep & friends
#
timestep                2.0
stepsPerCycle           8
nonBondedFreq           2
fullElectFrequency      4

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

#
# Basic dynamics
#
temperature             0
COMmotion               no
dielectric              1.0
exclude                 scaled1-4
1-4scaling              1.0
rigidbonds              all

#
# Particle Mesh Ewald parameters. 
#
Pme                     on
PmeGridsizeX            80                      # <===== CHANGE ME
PmeGridsizeY            64                      # <===== CHANGE ME
PmeGridsizeZ            60                      # <===== CHANGE ME


#
# Periodic boundary things
#
wrapWater               on
wrapNearest             on

cellBasisVector1        78.59   00.00   00.00   # <===== CHANGE ME
cellBasisVector2        00.00   60.14   00.00   # <===== CHANGE ME
cellBasisVector3        00.00   00.00   56.83   # <===== CHANGE ME
cellOrigin               0.02   -0.01    2.42   # <===== CHANGE ME

#
# Fixed atoms for initial heating-up steps
#
fixedAtoms              on
fixedAtomsForces        on
fixedAtomsFile          fix_backbone.pdb
fixedAtomsCol           B

#
# Restrained atoms for initial heating-up steps
#
constraints             on
consRef                 restrain_ca.pdb
consKFile               restrain_ca.pdb
consKCol                B

#
# Langevin dynamics parameters
#
langevin                on
langevinDamping         10
langevinTemp            320                     # <===== Check me
langevinHydrogen        on

langevinPiston          on
langevinPistonTarget    1.01325
langevinPistonPeriod    200
langevinPistonDecay     100
langevinPistonTemp      320                     # <===== Check me

useGroupPressure        yes


##########################################
# The actual minimisation and heating-up 
# protocol follows. The number of steps
# shown below are too small for a real run
##########################################

#
# run one step to get into scripting mode
#
minimize                0

#
# turn off pressure control until later
#
langevinPiston          off

#
# minimize nonbackbone atoms
#
minimize                2000                    ;# <===== CHANGE ME
output                  output/min_fix

#
# min all atoms
#
fixedAtoms              off
minimize                2000                    ;# <===== CHANGE ME
output                  output/min_all

#
# heat with CAs restrained
#
set temp 20;
while { $temp < 321 } {                         ;# <===== Check me
langevinTemp            $temp
run                     2000                   ;# <===== CHANGE ME
output                  output/heat_ca
set temp [expr $temp + 20]                      
}

#
# equilibrate volume with CAs restrained
#
langevinPiston          on
run                     10000                   ;# <===== CHANGE ME
output                  output/equil_ca

#
# equilibrate volume without restraints
#
constraintScaling       0
run                     100000                   ;# <===== CHANGE ME