Yes you are correct
On Tue, Jul 16, 2024, 2:10 AM Nitin Kulhar via AMBER <amber.ambermd.org>
wrote:
> Dear all
>
> I am writing to seek clarification on an (apparent) discrepancy in the
> Amber22 user manual and
> the tutorial on constant pH MD
> <https://ambermd.org/tutorials/advanced/tutorial18/section1.php>.
>
> The manual indicates that (A) *tautp* controls the
> heat bath coupling in the "weak-coupling ensemble"
> scheme invoked by *ntt=1* and that (B) *gamma_ln* controls
> the coupling in the Langevin scheme invoked by *ntt=3*.
>
> The tutorial, on the other hand, uses both *tautp* and
> *gamma_ln* with *ntt=3*.
>
> The original article <https://doi.org/10.1002/jcc.20139> on constant pH MD
> in the
> generalized Born framework uses the Berendsen
> thermostat (*ntt=11*) with *tautp=2*, consistent with
> the manual.
>
> Am I correct in assuming that the MD engine
> ignores *tautp* when it finds *ntt *set to* 3*?
>
> Thanks and regards
> Nitin Kulhar
> PhD student
> c/o Prof Rajakumara Eerappa
> Macromolecular Structural Biology Group
> Indian Institute of Technology Hyderabad (IITH)
> Kandi, Sangareddy
> Telangana, India (502 284)
>
> --
>
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Received on Tue Jul 16 2024 - 04:00:02 PDT
