On Thu, Sep 13, 2012 at 9:36 AM, Cheng-I Lee <biocil.ccu.edu.tw> wrote:
> Dear Amber users,
>
> Is *constant-pH* replica-exchange molecular dynamics available in Amber 12?
>
It depends on the variant you are talking about. The one detailed here:
http://pubs.acs.org/doi/abs/10.1021/jp303385x utilizes Hamiltonian replica
exchange with each replica at a different pH (and H-REMD is implemented in
Amber 12).
The one detailed here: http://pubs.acs.org/doi/abs/10.1021/ct300512h I
implemented after Amber 12 was released (and will therefore be part of
Amber 13). (If you have more than 3 titratable residues, this one tends to
work better.)
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 13 2012 - 08:00:02 PDT
