MBG wiki: equilibration NAMD script

structure               ionized.psf
coordinates             heat_out.coor
velocities              heat_out.vel
extendedSystem          heat_out.xsc
parameters              parallh22x.pro
parameters              water+ions.par

restartname             output/restart
restartfreq             1000
binaryrestart           yes

outputEnergies          20
outputTiming            200
xstFreq                 200
dcdFreq                 200
wrapWater               on
wrapNearest             on
wrapAll                 on

timestep                2
rigidbonds              all
nonBondedFreq           2
fullElectFrequency      4
stepsPerCycle           8

switching               on
switchDist              10
cutoff                  12      
pairlistdist            13.5

Pme                     on
PmeGridsizeX            128 #grid for fft
PmeGridsizeY            80  #grid for fft       
PmeGridsizeZ            64  #grid for fft 

exclude                 scaled1-4
1-4scaling              1.0

langevin                on
langevinDamping         1
langevinTemp            320
langevinHydrogen        on

langevinPiston          on
langevinPistonTarget    1.01325
langevinPistonPeriod    200
langevinPistonDecay     500
langevinPistonTemp      320

useGroupPressure        yes

binaryoutput            off
outputname              output/equi_out

firsttimestep           120000
run                     3000000