Hi, I am a new user of Namd, and I met some problems using increment of temperature during simulation

From: Ye Yang (knightyangpku_at_gmail.com)
Date: Fri Feb 25 2011 - 13:40:43 CST

Hi,
      I am a new user of Namd. When I use temperature
reassignment/temperature increment, I met some problems:
      I am trying to heat up the protein in the waterbox to see its
unfolding by temperature increment from 310K.
      It seems to be that I cannot use Langevin dynamics in this way, since
it is at constant temperature: When I use it, the temperature just do not
increase, and it does not unfold.
      So I deleted the Langevin dynamics in the configuration file. However,
when I did this, and extend the simulation time, I found the protein just
moved out of the water box even before the first heating up
step(translational movement). Also, the temperature is around 180K, which is
very wield. Is there any way to solve this problem(I used wrap water, maybe
wrap all this time)? Or is there any possibility to use Langevin dynamics
while increasing the temperature?
      Thank you very much.

Ye

Mechanical Engineering
Duke University

The config file goes as follows:
      #############################################################
## JOB DESCRIPTION ##
#############################################################

# Equilibration of ConAnk-mut structure
#
# EQ NI3C-mut H85R
# 031110
# NI3C-mut85-smd.ref

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################

structure NI3C_wb.psf
coordinates NI3C_wb.pdb

set temperature 310
set outputname Ni3C

# Continuing a job from the restart files
if {0} {
set inputname Mineq-G2a
BinCoordinates $inputname.restart.coor
#BinVelocities $inputname.restart.vel ;# remove the "temperature"
entry if you use this!
ExtendedSystem $inputname.xsc
firsttimestep 0
} else {
firsttimestep 0
}

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

# Input
paraTypeCharmm on
parameters par_all27_prot_lipid.inp
temperature $temperature

# Periodic Boundary conditions
if {1} {
cellBasisVector1 101.1 0. 0.
cellBasisVector2 0. 95.76 0.
cellBasisVector3 0. 0 109.2
cellOrigin 8.31 23.26 1.27
}

wrapWater on
wrapAll off

# 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 2
fullElectFrequency 4
stepspercycle 20

#PME (for full-system periodic electrostatics, choose prime multiples)
if {1} {
PME yes
PMEGridSizeX 120 ; #2*2*5*5
PMEGridSizeY 100 ; #
PMEGridSizeZ 120 ;#
PMEpencils 1
}

# Constant Temperature Control
#if {1}
#{
#langevin on ;# do langevin dynamics
#langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
#langevinTemp $temperature
#langevinHydrogen no ;# don't couple langevin bath to hydrogens
#}

# Constant Pressure Control (variable volume)
if {1} {
useGroupPressure no ;# needed for 2fs steps
useFlexibleCell no ;# x-y-z flexible
useConstantArea no ;# fix x-y plane, z in motion

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature
}

# Output
outputName $outputname
restartname $outputname.restart
dcdfile $outputname.dcd
xstFile $outputname.xst
velDCDfile $outputname.vel.dcd

restartfreq 20000 ;# 20000steps = every 20ps
dcdfreq 5000
xstFreq 1000
velDCDFreq 1000
outputEnergies 1000
outputPressure 1000

# Fixed Atoms Constraint (set PDB beta-column to 1)
if {0} {
fixedAtoms on
fixedAtomsForces on
fixedAtomsFile NI3C-mut85-smd.ref
fixedAtomsCol B
}

# Fixed Atoms Constraint (alternate method, Beta column = spr constant k)
if {0} {
constraints on
consKCol B
consref GB1fibr2a_wb-fixed.pdb
consKFile GB1fibr2a_wb-fixed.pdb
}

# Hydrogen Bond Constraints
if {0} {
freeEnergy On
freeEnergyConfig Hbondconstr6.namd
}

# IMD Settings (can view sim in VMD)
if {0} {
IMDon on
IMDport 3000 ;# port number (enter it in VMD)
IMDfreq 1 ;# send every 1 frame
IMDwait no ;# wait for VMD to connect before running?
}

#############################################################
## EXTRA PARAMETERS ##
#############################################################
# Add this part
# Put here any custom parameters that are specific to
# this job (e.g., SMD, TclForces, etc...)
#temperature reassign
reassignFreq 2000000 ;#2ns
reassignIncr 10
reassignHold 374

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

# Minimization

if {1} {
minimize 50000
reinitvels $temperature
}
run 20000000 ;

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