[gmx-users] Stochastic Dynamics nsttcouple

[Christian Blau]

Hi John,


Thanks for the suggestion! Find a patch here that updates the mdp documentation to clarify the issue you had with nsttcoupl:

https://gerrit.gromacs.org/c/gromacs/+/14157


Let me know if things are still unclear.


Best,

Christian

On 11/7/19 1:38 PM, John Whittaker wrote:
> 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
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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>