tut2.namd

set outputname 		tut2-run
set temperature		310
structure		solvate.psf
coordinates		solvate.pdb
paraTypeCharmm	on
parameters		par_all27_prot_lipid_na.inp
temperature		$temperature

exclude             scaled1-4
1-4scaling          1.0
cutoff              12.0
switching           on
switchdist          10.0
pairlistdist        14.0
timestep            2.0  ;# 2fs/step
rigidBonds          all  ;# rattle algorithm
nonbondedFreq       1
fullElectFrequency  2
stepspercycle       10
langevin            on    ;# do langevin dynamics
langevinDamping     1     ;# damping coefficient (gamma) of 1/ps
langevinTemp        $temperature
langevinHydrogen    off    ;# don't couple langevin bath to hydrogens
useGroupPressure      yes ;# needed for rigidBonds
useFlexibleCell       yes ;#useful for membrane simulations. Set to no for soluble proteins
useConstantArea       no
langevinPiston        on
langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
langevinPistonPeriod  100.0
langevinPistonDecay   50.0
langevinPistonTemp    $temperature
cellBasisVector1    61.56700000166893     0.0     0.0
cellBasisVector2     0.0     62.361998319625854    0.0
cellBasisVector3     0.0      0.0     66.26399803161621
cellOrigin           30.821117401123047    29.162376403808594     17.781869888305664
wrapAll             on
PME                 yes
PMEGridSpacing      1.0

outputName          $outputname
restartfreq         100
dcdfreq             100
xstFreq             100
outputEnergies      100
outputPressure      100

IMDon           on
IMDport         3000    ;# port number (enter it in VMD)
IMDfreq         1       ;# send every 1 frame
IMDwait         no     ;# wait for VMD to connect before running?
minimize            500
run            	   10000