[gmx-users] help with REMD

[Mark Abraham]

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