restarting calc giving new temperatures

From: Magnus Heltstrom (mheltstrom_at_gmail.com)
Date: Fri Feb 22 2008 - 14:39:58 CST

Hi,

I try to restart my calculation but the temperature has changed from ~ 301 K
to 201 K. The temperature raises for the next 20.000 steps and equilibrate
around 294 K which should be 300 K. This I find rather strange..... My
restart file looks like this

set path par_all27_prot_na.prm

# set PDB and PSF file
set pdb min_solvent.pdb
set psf sol_pep.psf

# Set number of MD steps 5ns
set md 12000000

# Freezing atoms for minimization
set fix 0
set pme 1
set nve 0
set npt 1

# Restarting simulation
set inputname min_whole_sys

Bincoordinates $inputname.restart.coor
Binvelocities $inputname.restart.vel
ExtendedSystem $inputname.restart.xsc

set firsttimestep 8312000

#################################
# Adjustable parameters
#################################

structure $psf
coordinates $pdb

outputName restart_Lder

##################################

restartfreq 500
dcdfreq 2000
xstFreq 500
outputEnergies 100
outputTiming 1000

#################################
# Simulation parameters
#################################

paraTypeCharmm on
parameters $path
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10
pairlistdist 14
stepspercycle 10
timestep 0.5
rigidBonds none
nonbondedFreq 1
fullElectFrequency 2

###################################
#
# Temperature and Pressure control
#
###################################
###################################
#
# Constant Temperature Control
#
###################################

if {$nve==0} {
langevin on
langevinDamping 5.
langevinTemp 300
langevinHydrogen no
}

if {$npt == 1} {
langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 100
langevinPistonDecay 50
LangevinPistonTemp 300
useGroupPressure yes ;# needed for rigid bonds
useFlexibleCell no ;# no for water box, yes for membrane
useConstantArea no ;# no for water box, maybe for membrane
}

wrapWater on
wrapAll on

if {$pme == 1} {
   PME yes
   PMEGridSizeX 64 ;
   PMEGridSizeY 64 ;
   PMEGridSizeZ 64 ;
}

run $md

How to resolve this and what is the problem? Furthermore, I try to set the
firsttimestep 8312000 but the log file starts at 0...

Any help or advise appreciated - many thanks.

Best Mag

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