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.chemdept.chem.ou.edu
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Received on Fri Apr 15 2005 - 22:53:01 PDT
