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

David van der Spoel spoel at xray.bmc.uu.se
Thu May 10 06:53:27 CEST 2007

Mark Abraham wrote:
> 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.

Usually you want to get the averages per temperature and then you don't 
need to demux, however in some case where you have good sampling you can 
use the "almost physical" trajectories including T jumps, as we showed 
in a paper last year: Phys. Rev. Lett. 96 pp. 238102 (2006)

> Mark
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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