MBG wiki: equilibration NAMD script for T40Y


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