RE: shape change of water box and peptide move out

From: Dong Luo (us917_at_yahoo.com)
Date: Mon Aug 15 2005 - 10:46:48 CDT

Constant pressure and langevin dynamics were not used.
By adding them back, the water box shape doesn't
change any more and peptide is not moving out as far
as 2 heat annealing cycle finished. But please help me
check my script file to see if there are any other
problems.

The input file:

structure babawb.psf
coordinates babawbmin.coor
set temperature 300
set outputname chlix1
firsttimestep 0

paraTypeCharmm on
parameters ../par_all27_prot_lipid.inp
temperature $temperature

exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 8.0
cutoff 12.0
pairlistdist 13.5

timestep 1.0
nonbondedFreq 2
fullElectFrequency 4
stepspercycle 20

cellBasisVector1 63. 0. 0.
cellBasisVector2 0. 52. 0.
cellBasisVector3 0. 0 39.
cellOrigin -22.04 7.85 -4.67
wrapAll on

PME yes
PMEGridSizeX 64
PMEGridSizeY 54
PMEGridSizeZ 40

outputName $outputname
restartfreq 500
dcdfreq 500
xstFreq 500
outputEnergies 500
outputPressure 500

langevin on
langevinDamping 5
langevinTemp $temperature
langevinHydrogen off

useGroupPressure yes
useFlexibleCell no
useConstantArea no

langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature

for { set TEMP 300 } { $TEMP <= 580 } { incr TEMP 10 }
{
  run 10000
  reinitvels $TEMP
  langevinTemp $TEMP
  langevinPistonTemp $TEMP
}
run 250000
for { set TEMP 570 } { $TEMP >= 300 } { incr TEMP -10
} {
  reinitvels $TEMP
  langevinTemp $TEMP
  langevinPistonTemp $TEMP
  run 20000
}

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