[gmx-users] g_sas and shuffled trajectory

Dallas Warren dallas.warren at vcp.monash.edu.au
Tue Apr 29 04:28:00 CEST 2003

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.

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.

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.

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.

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.

Am I missing something here, or is it not possible for me to analyse this 

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy
Monash University
381 Royal Parade
Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083
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