[gmx-users] g_gyrate

Dallas Warren dallas.warren at vcp.monash.edu.au
Tue Sep 30 01:35:01 CEST 2003

>You can still first do it 'manually' with trjconv, with the added advantage
>that it only has to be done once, and you can check if it is done the way
>you expect it to. Having said that, the last time I tried either -pbc nojump,
>or the 'cluster' option, it didn't work the way I expected (but I also did
>not have time then to get to the bottom of it).

Yeah, I have some trajectories where it does an OK job, others where I have 
tried so many options and combinations to try and get it to get things all 
together in the center of the box, to no avail.

What I was actually suggesting is that the scripts can go over the pbc, out 
one side and in the other, as if it was within the box.  Since it is 
continuous anyway with the simulation, shouldn't it also be with the 
analysis scripts?

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
When the only tool you own is a hammer, every problem begins to resemble a nail.
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