Output temperature not agreeing with tcouple temperature

From: Karson Bader (Qphysicist_at_hotmail.com)
Date: Fri May 13 2016 - 12:07:52 CDT


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.






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


minimize 1000

reinitvels $temperature

run 100000

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