(no subject)

From: Madhulika Gupta (gmadhulika1909_at_gmail.com)
Date: Tue Jan 24 2012 - 23:08:52 CST

Dear All
I have beta-hairpin which I am trying to cool from 400K to 300K at
rate of 1K per 2500 steps but on plotting temperature vs timestep, my
temperature does not reduce by 1K for every 2500 steps, infact the
temperature comes to 300K by 20-25K jumps at about 10,000 and remains
the same till the last timestep. I also tried using a loop to cool
from 400-390K at rate of 1K per 2500steps by changing
langevinPistonTemp, reassigntemp at each Kelvin but even that doesnot
show a proper cooling ramp. I am attaching both files, any advices
would be of great help.

1. cooling from 400-300K
structure ../../../../common/hairpin_wbionize.psf
coordinates ../../../prod-4ns/beta.400.nve.coor

set temperature 400
set outputname beta.cool4ns.5

firsttimestep 0
seed 3000

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input
paraTypeCharmm on
parameters ../../../../common/par_all27_prot_lipid.inp
temperature $temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 18.
switching on
switchdist 16.
pairlistdist 19.5

#Reassign parameters fro cooling
reassignFreq 2500
reassignIncr 1
reassignHold 300

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20
rigidTolerance 0.00001
rigidIterations 100

#constant pressure control
useGroupPressure yes
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1
langevinPistonperiod 100
langevinPistonDecay 50
langevinPistonTemp 300

# Periodic Boundary Conditions
extendedSystem ../../../prod-4ns/beta.400.nve.more.xsc

wrapAll on
wrapWater on

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 40
PMEGridSizeY 40
PMEGridSizeZ 40

# Output
outputName $outputname

restartfreq 1000 ;# 1000steps = every 1ps
dcdfreq 2500
xstFreq 500
outputEnergies 100
outputPressure 100
outputTiming 500

#############################################################
## EXTRA PARAMETERS ##
#############################################################
binaryoutput no
binaryrestart yes

#############################################################
## EXECUTION SCRIPT ##
#############################################################

# Minimization
numsteps 300000

2. Cooling from 400-390K
structure ../../common/hairpin_wbionize.psf
coordinates ../../4ns-more/beta.400.nve.more.coor

set temperature 400
set outputname beta.400-390.vel.intscr

firsttimestep 0
seed 3000

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input
paraTypeCharmm on
parameters ../../common/par_all27_prot_lipid.inp
temperature $temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 18.
switching on
switchdist 16.
pairlistdist 19.5

#Reassign parameters
reassignFreq 2500
reassignHold 390
reassignIncr 1

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
rigidTolerance 0.00001
rigidIterations 100

#constant pressure control
useGroupPressure yes
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1
langevinPistonperiod 100
langevinPistonDecay 50

# Periodic Boundary Conditions
extendedSystem ../../4ns-more/beta.400.nve.more.restart.xsc

wrapAll on
wrapWater on

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 40
PMEGridSizeY 40
PMEGridSizeZ 40

# Output
outputName $outputname

restartfreq 1000 ;# 1000steps = every 1ps
dcdfreq 25
xstFreq 500
outputEnergies 1
outputPressure 1
outputTiming 50

#############################################################
## EXTRA PARAMETERS ##
#############################################################
binaryoutput no
binaryrestart yes

#############################################################
## EXECUTION SCRIPT ##
#############################################################

# Minimization
set freq 2500

for {set i 400} {$i >= 390} {incr i} {
langevinPistonTemp $i
reassignTemp $i
reinitvels $i
run $freq
  }
run 5000

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