Dear all, I am new to doing replica exchange simulations. I am trying to understand the empirical transition matrix printed in the log files. I tried exchange intervals 2 ps and 0.2 ps. However, later I read gromacs recommends exchange interval not to be under 1ps. The system is protein in water and I am only showing parts of the matrix:
Exchange interval: 0.2 ps Repl 1 2 3 4 5 Repl 0.9528 0.0472 0.0000 0.0000 0.0000 Repl 0.0472 0.9017 0.0511 0.0000 0.0000 Repl 0.0000 0.0511 0.8946 0.0543 0.0000 Repl 0.0000 0.0000 0.0543 0.8898 0.0558 1. If I look at line 3 ""Repl 0.0472 0.9017 0.0511" does this mean exchange between replica 1, 2 is accepted 4.72 % and exchange between 2,3 is accepted 5.11 % ? Repl 1 2 3 4 5 Repl 0.9504 0.0496 0.0000 0.0000 0.0000 Repl 0.0496 0.8982 0.0522 0.0000 0.0000 Repl 0.0000 0.0522 0.8942 0.0536 0.0000 Repl 0.0000 0.0000 0.0536 0.8888 0.0576 2. With exchange interval 2 ps, I am getting slightly better acceptance rate. For example, again looking at line 3 "Repl 0.0496 0.8982 0.0522" the acceptance rate for exchange 1 to 2 is 4.96 %, and he acceptance rate for exchange 2 to 3 is 5.22 % thanks, Shyno -- Shyno Mathew PhD Candidate Department of Chemical Engineering Graduate Assistant Office of Graduate Student Affairs The Fu Foundation School Of Engineering and Applied Science Columbia University -- 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.
