Re: Adaptive tempering implementation in NAMD differs

From: Sachin Natesh (snatesh_at_uchicago.edu)
Date: Thu Sep 24 2015 - 20:28:36 CDT

Hi Nicholas,

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? 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. I haven't looked at the
cumulative distribution of temperatures, though will check and see if I get
1/B form. All of my temperature bins (1000) seem to be populated at some
point in the sim. Might you know of any way to use adaptive tempering in
NAMD as it is done in the paper and GROMACS? (i.e. potential rescaling).

Best,
Sachin

On Wed, Sep 23, 2015 at 11:51 AM, Nicholas M. Glykos <glykos_at_mbg.duth.gr>
wrote:

>
> I'm doing adaptive tempering through the Langevin thermostat which
> smooths-out
> temperature changes. As far as I remember I have only seen such abrupt
> changes at the very beginning of the simulation (before accumulation of
> an adequate number of samples). Have you looked at the cumulative
> distribution of temperatures ? If you have a sufficient number of samples,
> it should tend to the (1/β) form. I'm sending you two graphs which
> correspond to a very small sample of a simulation : the first is the
> variation of temperature vs time with successive data points corresponding
> to a Δt of 0.8 ps. The second is the cumulative temperature distribution
> for the same period of time. Other than that, no idea.
>
>
>
>
> Στις 23-09-2015 18:28, Sachin Natesh έγραψε:
>
>> 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?
>>
>> Best,
>> Sachin
>>
>> On Wed, Sep 23, 2015 at 5:45 AM, Nicholas M. Glykos
>> <glykos_at_mbg.duth.gr> wrote:
>>
>> 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 [1],
>>> Ext.77620, Tel (lab) +302551030615 [2],
>>> http://utopia.duth.gr/glykos/ [3]
>>>
>>
>>
>>
>> Links:
>> ------
>> [1] tel:%2B302551030620
>> [2] tel:%2B302551030615
>> [3] http://utopia.duth.gr/glykos/
>>
>
> --
> 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/
>


tempvtime_sim2_ubq.png

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