[gmx-users] Another shuffling question ..
baaden at smplinux.de
Wed May 1 14:04:16 CEST 2002
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
should you use for analysis (or does it make no difference) ?
Sorry if these are trivial questions.
Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
mailto:baaden at smplinux.de - ICQ# 11466242 - http://www.marc-baaden.de
FAX/Voice +49 697912 39550 - Tel: +44 1865 275380 or +33 609 843217
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