[gmx-users] REMD

[David van der Spoel]

merc mertens wrote:
>>> 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.
> 
> this is what i did (using gromacs 3.3.1):
> 
> trjcat -f traj*.trr -o j.trr -demux remd.xvg
> 
> trjcat reads:
> traj0.trr, traj1.trr - traj11.trr
> 
> and remd.xvg contains lines like:
>  0 0 1 2 3 4 5 6 7 8 9 10 11
>  1 0 1 2 3 5 4 6 7 8 9 11 10     
>  2 0 1 2 3 4 5 6 8 7 10 9 11     
>  3 0 1 2 3 4 5 6 7 8 9 10 11     
>  4 0 1 2 3 4 5 6 7 8 9 10 11     
>  5 0 1 2 3 4 5 6 7 8 9 10 11     
>  6 0 1 2 3 4 5 6 7 8 9 10 11     
>  7 0 1 2 3 4 5 7 6 8 9 10 11     
>  8 0 1 2 3 4 5 6 7 8 9 10 11     
>  9 0 1 3 2 4 5 6 7 8 9 10 11     
> 
> remd.xvg was build like described above. output is only one trajectory, containing only box information.
> 
> additionally i tried:
> 
> trjcat -f traj0.trr traj1.trr traj2.trr ... -o j0.xtc j1.xtc j2.xtc ... -demux remd.xvg
> 
> but from that i got only one trajectory as output, too (also only containing box info).
How about the trr files? Are they written with the same frequency as 
what you have in the remd.xvg file? Otherwise I don't know what will 
happen...

-- 
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://folding.bmc.uu.se
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