[gmx-users] Question on analyzing REMD simulation

[Mark Abraham]

N-J.M. Macaluso wrote:
> Hello,
> 
>    Thanks for your responses on the demux.pl script. I have some more 
> basic questions on how to analyze an REMD simulation in Gromacs.
> 
> (1) How can I find the acceptance ratio? 

Look carefully at the output in the log file :-) You will need to do 
some averaging over log files if you ran more than one job for the 
simulation.

(2) Does anyone know how to
> graph the temperature or potential energy of a single replica as a 
> function of time?

Yup, write it down and graph it. :-)

Seriously, though, I (and doubtless others) have perl scripts that do 
tasks like these when fed a set of .log files. I'm not interested in 
following single replicas, so they wouldn't be any good to you unless 
you can modify them.

There were some van der Spoel scripts that he threatened to publish on 
the webpage a year or more ago... have they seen the light of day David?

Mark