Re: Adaptive tempering implementation in NAMD differs

From: Sachin Natesh (
Date: Wed Sep 23 2015 - 10:28:05 CDT

Hi Nicholas,

I spoke with a member of Ma's group and was shown a few plots of the
adaptive temperature for simulations he had run. They were all similar to
what is seen in Fig.6 of the paper. However, the local behavior of the
temperature showed a far more gradual rate of change than what I am
observing for system temperature from adaptive tempering in NAMD. There
were no instances (at least that I saw) where the temperature changed by
large amounts (eg. 100K) in under a picosecond. I suspect that this local
behavior can also be seen in Fig.6 if we could 'enhance' the view along
time axis. Have you any thoughts on this?


On Wed, Sep 23, 2015 at 5:45 AM, Nicholas M. Glykos <>

> I ask because I've noticed extremely
>> rapid and large changes in the system temperature (over 100K in under 1000
>> fs) for simulations in which I have tempering turned on.
> Which is consistent with the behavior of the temperature also seen
> in Fig.6 of the Zhang & Ma paper (see 'Trajectory I').
> --
> 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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