Rebeca García Fandiño wrote:
Hello,
I am trying to do REMD for a protein unfolding. I am following the
information given in http://wiki.gromacs.org/index.php/REMD but I am
completely new in these type of simulations. I would like to ask
two questions to more advanced users. I hope you could help me:
-I have seen that the exchange rate should be typically between 0.2 and
0.3. Where can I extract the exchange rate from my outputs? For example
in the output below the exchange rate would be "Repl pr .08
.00 .13"? Should I calculate a mean for all exchanges and all
replicas and check if this mean is between 0.2 and 0.3?
No, you should look at the end of the .log output, where these averages
are reported. I suspect these are only averages for that invocation of
mdrun for GROMACS versions 3.3.x, and have no idea about 4.0.x.
Repl 0 <-> 1 dE = 2.492e+00
Repl ex 0 1 2 3 4 5
Repl pr .08 .00 .13
Replica exchange at step 2000 time 4
Repl ex 0 1 2 3 x 4 5
Repl pr .00 1.0
-Another question is about restarting simulations. I have though doing
it with tpbconv and then concatenate the .log files to use demux.pl. Is
this correct?
Under 3.3.x, yes tpbconv is the way to do restarts. Using demux.pl is a
separate issue. See the wiki page on restarts.
Mark
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