From: Nicholas M Glykos (glykos_at_mbg.duth.gr)
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, http://utopia.duth.gr/glykos/
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