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 Mon Jul 15 2024 - 23:30:02 PDT
