From: §³henyi (cy_liao_at_foxmail.com)
Date: Thu Jun 09 2016 - 15:17:25 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, there are distinct values 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: 321.084
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSING GPRESSAVG
ENERGY: 0 3561.5822 17228.7267 10530.9700 242.6606 -93990.9995 -25.8461 0.0000 0.0000 40188.0505 -22264.8555 408.3090 -62452.9060 -21956.2091 408.3090 1590.4135 1593.3703 437626.8884 1590.4135 1593.3703
...
ADAPTEMP: WRITING RESTART FILE AT STEP 20000
ADAPTEMP: STEP 20000 TEMP 334.6136257 ENERGY -63046.83531 ENERGYAVG -62421.61117 ENERGYVAR 1580249.38
#---------------------
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 on;
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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