[gmx-users] help with REMD
Mark.Abraham at anu.edu.au
Mon Jan 12 13:12:28 CET 2009
Rebeca García Fandiño wrote:
> 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.
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