[gmx-users] Stochastic Dynamics nsttcouple

[John Whittaker]

Hi Justin,

Thank you very much for the response. That's the conclusion I kept coming
to, but I'm happy to know it for sure now.

I'm not sure if others have been confused by this in the past, but it
would have saved me some trouble had I known that explicitly from the
beginning; any chance this note can be added to the documentation (at
least the mdp options page)?

Thanks again,

John

>
>
> On 11/6/19 10:40 AM, John Whittaker wrote:
>> Hi all,
>>
>> Please correct me if this is the wrong list for this particular
>> question.
>>
>> I have been messing around with the stochastic dynamics integrator in
>> version 5.1 (yes, it's relatively ancient, but I am testing some things
>> involving AdResS) and I can't wrap my head around something:
>>
>> In the src/gromacs/mdlib/update.cpp file, I cannot find a moment when
>> the
>> parameter "nsttcouple" is used in order to determine when the thermostat
>> is applied. I'm not sure if this is a stupid question, but are the
>> friction and noise applied at each step, regardless of the value of
>> nsttcouple?
>>
>> I understand that tcoupl is ignored when the SD integrator is used, but
>> does this mean that nsttcouple is ignored, too?
>
> Yes. Formally, the SD integrator does not apply an explicit thermostat
> algorithm; velocities are updated based on the friction coefficient
> specified in the .mdp file. nsttcoupl is only relevant when tcoupl is
> active, which it is not when using SD.
>
> -Justin
>
>> I am by no means an expert in C++ so I could have easily misunderstood
>> or
>> missed something, but this question has been plaguing me for a couple
>> days. Any help I can get to better understand this is much appreciated!
>>
>> Best,
>>
>> John
>>
>>
>>
>>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
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