From: Karson Bader (Qphysicist_at_hotmail.com)
Date: Fri May 13 2016 - 12:07:52 CDT
Hello,
I have a 6 layer graphite system. The bottom three are completely fixed, the 4th layer Carbon atoms are attached to a heat bath with the outer most atoms of the 4th later fixed. The 5th and 6th layers have their outer most atoms fixed to prevent them from drifting away and the inner atoms are free to move. A basic diagram is below, where Xs are fixed, Os are free but allowed to move and 1s are the atoms coupled to the heat bath.
xooooox
xooooox
x11111x
xxxxxxx
xxxxxxx
When I look at the temperature data from the output file, the system temperature agrees with what I have in the configuration file, but when I look at the temperature of each individual layer (by using a custom script) the coupled layer is much higher (140-150K) with layers 5 and 6 being between 50-70K. The overal average of of the layers agrees with the configuration file temp.
I'm guessing that when the program checks the temperature it looks at ALL moving atoms, not just the layer that is coupled to the heat bath.
Is there a way assign a temperature to only a subset of atoms and have ONLY those atoms looked at when the temperature is being checked?
Extra info:
I am using two different files to assign fixed atoms and tcoupled atoms.
My configuration file is below:
#namd configuration file
#Job Description
#Adjustable Parameters
structure C60_sim.psf
coordinates C60_sim.pdb
outputname output
set temperature 80
firsttimestep 0
#Simulation Parameters
paraTypeCharmm on
parameters C60.params
temperature $temperature
#Periodic Boundary Conditions
cellBasisVector1 42.6 0.00 0.00
cellBasisVector2 0.00 36.9 0.00
wrapAll off
wrapNearest off
#numsteps 1000
#Force-Field Parameters
exclude 1-4
1-4scaling 0.4
cutoff 10.8
switching off
switchdist 7.0
pairlistdist 12.8
margin 1.0
stepspercycle 2
#Integrator Parameters
#numsteps 1000
timestep 0.3
rigidBonds none
restartname C60.restart
restartfreq 100000
DCDfile Couple.dcd
DCDfreq 1
velDCDfile CoupleVel.dcd
velDCDfreq 1
binaryoutput no
outputEnergies 100
outputPressure 100
#Fixed Atoms Constraint
fixedAtoms on
fixedAtomsForces off
fixedAtomsFile C60_sim.pdb
fixedAtomsCol O
#Berendsen Temperature Control
tCouple on
tCoupleTemp $temperature
tCoupleFile C60_sim.pdb
tCoupleCol B
#Execution Script
#Minimization
minimize 1000
reinitvels $temperature
run 100000
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