[gmx-users] HREX simulation

[Shyno Mathew]

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