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.
________________________________________________________________________
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
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