[gmx-users] REMD

[David van der Spoel]

On Tue, 11 Jul 2006, merc mertens wrote:

>
>> you do need this option  (-demux) and the xvg file should hold N+1 columns
>> containing the correct permutation of replicas, e.g.
>> 
>> time repl 0 1 2 3  ...
>> 0     0   1   2   3
>> 1     1   0   2   3
>> 2     1   2   0   3
>> 
>> and so on
>
>so, if i observe in md.log an exchange like:
>"Repl ex  0    1    2 x   3" for e.g. time step 1
>that would convert into:
>"1      0   1   3   2"
>for remd.xvg. is that correct?
>the problem is, if i do something like this for the entire time scale trjcat only outputs the simulation box but no coordinates to the new trajectory. 
>

details please.
do you give trjcat N trajectories? then you should get N back as well.
give your entire command line and a snippet from the xvg file.

>
>
>

-- 
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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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