[gmx-users] shuffled option for parallel run

[Hector Martinez-Seara Monne]

Hi all,
I want to thank in advance everyone for the quick answers that you've 
been always giving me.
Now I have started running simulation of  monolayers in parallel. And 
I've found some things that I can't understand with the information that 
is given by the manual. I also been looking in the posts but I can't 
find the answer also. Well the main problem that I have is with the 
-deshuf option of grompp that the manual says is highly recommended. In 
fact the problem is that I can not understand what means really this 
option, and the most important that I don't know how to continue the 
simulation. I normally use "tpbconv" for generating the new *.tpr file, 
but know as I know that the file is shuffle I don't know if I need to 
add the option -n deshuf.ndx or instead don't use it and the index file 
will be for all the dynamic the same.
I'm wondering also if the use of this option change in any way the 
results except the trajectory, that I have to deshuffle with trjconv, 
and then it require extra work.

Thank you,

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     Hector Martínez-Seara Monné

      Universidad de Barcelona
         Dept. Química Fisica

          hseara at netscape.net
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