From: Marcelo Puiatti (marcelo.puiatti_at_gmail.com)
Date: Wed Jun 17 2009 - 15:27:18 CDT
Dear all:
I'm trying to perform a couple of MD runs varying the temperature from
50 K to 300 K.
I've read the manual and I add this lines to the config file:
reassignFreq 100
reassignTemp $temperature
reassignIncr 5
reassignHold 300
but after I read the output file with the Namd-plot pluggin with VMD
the system is always at the final temperature.
I'll apreciate any help, I attached here a copy of my config file.
Thank's in advance
Marcelo
#############################################################
## JOB DESCRIPTION ##
#############################################################
coordinates ../ntv.pdb
outputName heat1
set temperature 300
# Continuing a job from the restart files
if {1} {
set inputname min-3
binCoordinates $inputname.restart.coor
# binVelocities $inputname.restart.vel ;# remove the
"temperature" entry if you use this!
extendedSystem $inputname.restart.xsc
}
firsttimestep 2500
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
paraTypeCharmm off
paratypeXplor off
amber on
parmfile ../adri.top
ambercoor ../adri.crd # chequear
# NOTE: Do not set the initial velocity temperature if you
# have also specified a .vel restart file!
temperature $temperature
# Periodic Boundary Conditions
# NOTE: Do not set the periodic cell basis if you have also
# specified an .xsc restart file!
if {0} {
cellBasisVector1 25. 0. 0.
cellBasisVector2 0. 25.3 0.
cellBasisVector3 0. 0. 24.3
cellOrigin -0.14 0.40 -0.39
}
wrapWater on
wrapAll on
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
# Integrator Parameters
timestep 1.0 ;# 1fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20
#PME (for full-system periodic electrostatics)
if {0} {
PME yes
PMEGridSizeX 32
PMEGridSizeY 32
PMEGridSizeZ 32
}
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen no ;# don't couple langevin bath to hydrogens
# Escalar la temperatura de 0 K a 300K
reassignFreq 100
reassignTemp $temperature
reassignIncr 5
reassignHold 500
# Constant Pressure Control (variable volume)
if {1} {
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 200.
langevinPistonDecay 50.
langevinPistonTemp $temperature
}
restartfreq 1000 ;# 1000steps = every 1ps
dcdfreq 1000
xstFreq 1000
outputEnergies 100
outputPressure 100
# Fixed Atoms Constraint (set PDB beta-column to 1)
if {0} {
fixedAtoms on
fixedAtomsFile nottails.fix.pdb
fixedAtomsCol B
fixedAtomsForces on
}
#############################################################
## EXTRA PARAMETERS ##
#############################################################
# Put here any custom parameters that are specific to
# this job (e.g., SMD, TclForces, etc...)
constraints on
consexp 3
consref ../adri-ntv.pdb
conskfile ../adri-ntv.pdb
conskcol O
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
if {0} {
minimize 1000
reinitvels $temperature
}
run 50000 ;# 0.050 ns
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