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I have a trajectory in which the shuffle/sort option has been used (and I
don't use this anymore since it did improve scaling very much and the
problems in subsequent analysis of the files). Now I am trying to
analyze it using g_sas.<br><br>
Using the trajectory file as it is written out and the topology file used
as the input to generate that trajectory, I get a segmentation
fault.<br><br>
If the trajectory is then deshuffled using the deshuffle index file
generated by grompp when the topology file is generated, then the warning
about inconsistency shifts etc appears, which isn't surprising since the
topology file is still shuffled.<br><br>
I found a couple of previous discussions on the analysis of shuffled
trajectories, but all has been said is that you can deshuffle using the
deshuffle index file generated. Also, someone did ask if you had to
also generate a deshuffled topology file and it appears that you
don't. Additionally, you should be able to use a shuffled index
file.<br><br>
I attempted to generate a deshuffled gro file to then use to produced a
deshuffled index file to use, however editconf gives a segmentation
fault.<br><br>
Am I missing something here, or is it not possible for me to analyse this
trajectory?<br><br>
Catch ya,<br>
<x-sigsep><p></x-sigsep>
<b>Dr. Dallas Warren<br>
</b><i>Research Fellow<br>
</i>Department of Pharmaceutical Biology and Pharmacology<br>
Victorian College of Pharmacy<br>
Monash University<br>
381 Royal Parade<br>
Parkville VIC 3010<br>
<font color="#0000FF"><u>dallas.warren@vcp.monash.edu.au<br>
</u></font>+61 3 9903 9083</html>