[gmx-users] Another shuffling question ..

[Marc Baaden]

Hi,

 From the previous discussion about working with shuffled trajectories
I got the message (correct me if I am wrong) that you should do a 

trjconv -n deshuffle [..]

to create a deshuffled trajectory. Now if you want to analyze this
trajectory, does it mean you also have to create an unshuffled topology
(tpr file) by repeating grompp without eg "-np 8 -shuffle -sort " options ?

My concern is that if somehow interactions got mixed up, this would be
quite difficult to spot .. wouldn't it ?

Also, are the -np and -sort flags relevant to this ?
Eg, if the actual run was with

grompp -np 8 -shuffle -sort

and you want to analyze the deshuffled trajectory, which of

grompp -np 8 -sort
grompp -np 8
grompp -sort

should you use for analysis (or does it make no difference) ?

Sorry if these are trivial questions.
  Marc

-- 
 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
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