[gmx-users] shuffling around

[Anton Feenstra]

Christian Kandt wrote:
> 
> Hi again!
> 
> I just had an inspiration and found the answer to my shuffling problem
> (thanks Frank!!!): When using -shuffle an index file named "deshuf.ndx"
> is generated. Choosing this as the -n index file and a simple trjconv
> conversion of the "shuffled" trajectory does the trick.

Yep, that is the solution, although it is actually a very dirty hack
for something that mdrun should be doing for you. It stems partially
from the separation in preprocessor (grompp) and md engine (mdrun)
that we have. Since we're planning on merging them in some sensible
way, we have not been looking for a better intermediat solution to 
the 'shuffling problem'.


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
| |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
| (    ) |-----------------------------------------------------------|
|  \__/  | "Shake Yourself" (YES)                                    |
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