Re: Adaptive tempering implementation in NAMD differs

From: Nicholas M Glykos (
Date: Fri Sep 25 2015 - 04:36:52 CDT

> Thank you for your help. Do you think you can send me a a copy of a config
> file for one of your adaptive tempering sims?

Nothing exciting there, the relevant parts look like this :


# Adaptive ...
adaptTempMD on
adaptTempTmin 300
adaptTempTmax 500
adaptTempBins 1000
adaptTempRestartFile output/restart.tempering
adaptTempRestartFreq 10000
adaptTempLangevin on
adaptTempRescaling off
adaptTempOutFreq 400


# Langevin dynamics parameters
langevin on
langevinDamping 1
langevinTemp 320
langevinHydrogen off

langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 400
langevinPistonDecay 200
langevinPistonTemp 320

useGroupPressure yes

firsttimestep 30000
run 100000000

> I've attached a graph of temperature vs. time for a 7ns simulation of
> ubiquitin in which I used the langevin thermostat with damping of 1 and
> coupled the adaptive temperature (in range [300,600]) to the langevin
> thermostat. For whatever reason, the temperature changes very abruptly
> at several times.

Depending on the size of the system you may want to test different values
for adaptTempDt (give it a try with a value of 0.00020).

It is probably not relevant, but I'm not using the latest version of NAMD
due to problems with GPUs. If this is a test you are doing, you can send
me the files for a run and I'll test it with the older NAMD version still
living here.

            Nicholas M. Glykos, Department of Molecular Biology
     and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
    Ext.77620, Tel (lab) +302551030615,

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