AMBER Archive (2005)

Subject: AMBER: the restart of replica exchange method (REM) simulations in AMBER8

From: Scott E. Boesch (sboesch_at_chemdept.chem.ou.edu)
Date: Fri Apr 15 2005 - 16:24:24 CDT

Dear all:

I run some replica exchange method (REM) simulations by using AMBER8.

In the mdin.000 file, I change irest = 0 to irest = 1 and ntx = 1 to ntx =
5. And the program reads
the restart file instead of inpcrd. I can restart REM simulations.
Unfortunately, the acceptance
ratio of exchange temperature decreases largely in the following
simulations. I am wondering whether
this problem can be solved by changing other input parameters.

It seems a difficult job to obtain a good, even acceptance ratio (>10%) in
REM. My simulations results indicate that they are largely dependent upon
the initial temperatures (TEMPI), time steps between exchange attempts
(NSTLIM), not only exchange temperatures (TEMP). However, even if I set
some initial conditions to make a good REM simulations, the above restart
problem make me feel discouraged.

Thanks a lot
Best
Zunnan Huang
znhuang_at_chemdept.chem.ou.edu

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