[gmx-users] help with REMD

[Rebeca García Fandiño]

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?Repl 0 <-> 1  dE =  2.492e+00Repl ex  0    1    2    3    4    5Repl pr   .08       .00       .13Replica exchange at step 2000 time 4Repl ex  0    1    2    3 x  4    5Repl 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?
 
Thank you very much for your help.
Best wishes, 
 
Rebeca Garcia
Parc Cientific of Barcelona
Barcelona University
regafan at hotmail.com
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