From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Mon Oct 23 2006 - 03:07:28 CDT
Hi all
I was trying to heat my system with Temperature reassignment method.
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure ../common/prodh_wb.psf
coordinates ../common/prodh_wb.pdb
set temperature 0
set outputname heating/prodh_wb_heat
if {1} {
set inputname min/prodh_wb_min
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel ;# remove the "temperature" entry
if you use this!
extendedSystem $inputname.xsc
}
firsttimestep 10000
#############################################################
## 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 12.0
switching on
switchdist 10.0
pairlistdist 13.5
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Constant Temperature Control
langevin off ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
#Temperature Reassignment Parameters
reassignFreq 10000
reassignTemp 0
reassignIncr 25
reassignHold 300
# Periodic Boundary Conditions
cellBasisVector1 -81.875 0.0 0.0
cellBasisVector2 0.0 -79.3840036392 0.0
cellBasisVector3 0.0 0.0 -81.5929965973
cellOrigin 5.72501993179 45.225315094 49.4890518188
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 82
PMEGridSizeY 80
PMEGridSizeZ 82
# Output
outputName $outputname
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 500
xstFreq 500
outputEnergies 250
outputPressure 250
outputTiming 1000
#############################################################
## EXTRA PARAMETERS ##
#############################################################
#les off
#lesFactor 10
#lesReduceTemp on
#lesReduceMass on
#lesCol B
constraints on
consexp 2
consref ../common/prodh_wb_ref10.pdb
conskfile ../common/prodh_wb_res10.pdb
conskcol B
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
#minimize 10000
reinitvels $temperature
run 120000 ;# 120ps
I was running my simulation for 120000 time step and theoretically this
script should assign the temperature of 300 K at 120000th time step.
although it is assigning the temperature of 300 K at 120000th time step but
after that temperature of the system keeps on decreasing up to 250 K. what
should i do to maintain the temperature of system at 300 K.
(I was thinking that since i am restarting my simulation at 10000 time step
so this script will automatically assign temperature of my system to 25 K at
the bigining of simulation. so 300 K will reach at 110000th time step and
there will be 10000 time step to equilibrate my system at 300 K.)
How can i maintain my system temperature at 300 K once it reached in
simulation without using langevin dynamics temperature control (since i am
using Temperature reassignment for temperature control, i can not use
langevian dynamics.)
thank you for help.
-- Dhiraj Kumar Srivastava Department of Chemistry University of Missouri-Columbia MO, 65211
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