[gmx-users] how to use demux.pl for REMD analysis

[Mark Abraham]

N-J.M. Macaluso wrote:
> Hello,
> 
>     I've been reading all of the archived questions on the analysis of 
> REMD in Gromacs, and I'm still a bit confused. It appears that the first 
> step is to use the demux.pl script to demultiplex the REMD trajectories. 
> How to use this script, and what exactly this is supposed to accomplish? 
> After this is finished, how do I trace the temperature evolution of a 
> single replica?

mdrun returns (discontinuous) trajectories for each temperature. Only if 
you don't want these is demux.pl "the first step". Somehow (read the 
archives or the script itself for details, I expect) you need to 
construct a .xvg file that describes the exchanges, and you can demux 
these trajectories to get non-physical but continuous trajectories of 
individual structures, if you want them.

Mark