The adaptTemp and Temp in Adaptive tempering

From: Chenyi L (lchenyi9725_at_gmail.com)
Date: Thu Jul 07 2016 - 19:51:03 CDT

Hi all,

I am recently running Adaptive tempering for a protein-membrane system
which is running fine.
What I am confused is the real temperature I should monitor for the system.

As shown in the output.log, they are distinct for adaptTemp in the
"ADAPTEMP:..." line and Temp in the "ENERGY:..." line:
#---------------------
Info: INITIALISING ADAPTIVE TEMPERING
Info: READING ADAPTIVE TEMPERING RESTART FILE
Info: ADAPTIVE TEMPERING: TEMPERATURE RANGE: [300,600] KELVIN
Info: ADAPTIVE TEMPERING: NUMBER OF BINS TO STORE POT. ENERGY: 1000
Info: ADAPTIVE TEMPERING: ADAPTIVE BIN AVERAGING PARAMETER: 0.1
Info: ADAPTIVE TEMPERING: SCALING CONSTANT FOR LANGEVIN TEMPERATURE
UPDATES: 0.01
Info: ADAPTIVE TEMPERING: INITIAL TEMPERATURE: 303.993
ETITLE: TS BOND ANGLE DIHED IMPRP
              ELECT VDW BOUNDARY MISC
 KINETIC TOTAL TEMP POTENTIAL TOTAL3
    * TEMPAVG* PRESSURE GPRESSURE VOLUME
PRESSAVG GPRESSAVG
ENERGY: 0 3590.0823 17034.4659 10566.4454 226.4935
        -94477.2934 507.6301 0.0000 0.0000
40665.6409 -21886.5353 *413.1613 * -62552.1762
 -21580.0461 413.1613 2175.1558 2173.7953
 437626.8884 2175.1558 2173.7953

....

ADAPTEMP: WRITING RESTART FILE AT STEP 640000
ADAPTEMP: STEP 640000* TEMP 335.3487118* ENERGY -62621.84916 ENERGYAVG
-62118.94047 ENERGYVAR 554137.4421
TIMING: 640000 CPU: 13855.9, 0.0226963/step Wall: 14007.5,
0.0228164/step, 122.701 hours remaining, 147.464844 MB of memory in use.
ENERGY: 640000 3661.3406 17036.6912 10470.9904 243.7735
        -94207.7506 123.2968 0.0000 0.0000
40437.6991 -22233.9590 *410.8455 * -62671.6582
 -21929.9079 413.8077 1691.3769 1699.4490
 437626.8884 1791.6531 1791.6910

#---------------------

Obviously, the Temp in the "ENERGY:..." line is mostly in a range of [400,
420] K, but the adaptTemp in the "ADAPTEMP:..." line varies spanning [300,
600] K.

My run.inp config is:
#---------------------
set temp 310;
outputEnergies 20000;

# Constant Temperature Control
langevin on; # langevin dynamics
langevinDamping 1.0; # damping coefficient of 1/ps (keep
low)
langevinTemp $temp; # random noise at this level
langevinHydrogen off; # don't couple bath to hydrogens

# Adaptive Tempering; Temperature Control must be on
# Need to specify either adaptTempInFile or all of {adaptTempTmin,
adaptTempTmax,adaptTempBins} if adaptTempMD is on.
adaptTempMD on;
adaptTempFreq 10;
#adaptTempTmin 300;
#adaptTempTmax 600;
#adaptTempBins 1000;
adaptTempDt 0.01;
adaptTempInFile $inputname.dat
adaptTempRestartFile $outputname.restart.dat
adaptTempRestartFreq 10000;
adaptTempLangevin on;
adaptTempRescaling off;
adaptTempOutFreq 10000;
adaptTempFirstStep 0;
adaptTempLastStep 20000000;
adaptTempCgamma 0.1;
adaptTempRandom on;
#---------------------

My question is which temperature I should consult for the system in
evolution of time?
I want to make the temperature-time plot similar to Fig. 6 of paper by
Zhang and Ma in J. Chem. Phys. 132, 244101 (2010).

Thanks you so much for any kind help.

Best,
Chenyi

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