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
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
a mail to gmx-users-requ...@gromacs.org.
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
