Hello Jason,
Indeed, until Amber16 only the Hamiltonian and Temperature dimensions were implemented in the MultiD-REMD module. However, in Amber18 the pH dimension is now available for MultiD-REMD simulations in both sander and pmemd. Please take a look at the Amber18 manual to see more information about it.
Best,
Vinícius Wilian D Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633<tel:+1(352)846-1633>
On Apr 20, 2018, at 2:09 PM, Jason Ku Wang <jwang198.stanford.edu<mailto:jwang198.stanford.edu>> wrote:
Hi AMBER Community!
In reading about multidimensional REMD capabilities on AMBER, I came across
this line:
"pH-REMD is not currently compatible with T-REMD in another dimension.
Also, H-REMD/pH-REMD simulations are not expected to work well.
pH-compatible temperature and umbrella exchange are planned for the
future." (Top of page 426, AMBER 16 Manual:
https://urldefense.proofpoint.com/v2/url?u=http-3A__ambermd.org_doc12_Amber16.pdf&d=DwIGaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=LIQu8OlVNKmzfbMg9_5FnKrt9-DrdQBJXyFyocKAWXc&m=7vwlK_Tt_iYwuDKNBlsz25KCUW0vLqJFhuiCmLY2DA4&s=8jNipleZCVslTkneJIwrntkRBvy8-E-AmJsyMWUsxq8&e=)
It seems like temperature x Hamiltonian M-REMD is the best option, but I'm
curious why pH-REMD is not compatible/not expected work well in tandem with
temperature or Hamiltonian dimensions (e.g. is the reason software or
scientific)?
Thanks so much - once again!
Jason
--
Jason Wang
Stanford University, Class of 2018
jwang198.stanford.edu<mailto:jwang198.stanford.edu>
ᐧ
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Received on Fri Apr 20 2018 - 12:30:01 PDT
