[gmx-users] g_bundle usage

jo hanna jfhanna at gmail.com
Fri Aug 31 20:00:17 CEST 2007


The protein in my simulations has two distinct domains and some interdomain
motion is seen on the simualtion timescale. I was wanting to define a helix
in domain 1 and one in domain 2 and track their movement relative to each
other. For this I was going to use g_bundle. I have tried this but I am
doing something wrong as I get the error:
Fatal error: The size of one of your index groups is not a multiple of n
I have defined the groups in my index file:
helix 1
helix 2
and after entering:
g_bundle -s md1.tpr -f protein.xtc -n index.ndx -tu ns  (I have also tried
with -na 2)
I use these groups as input to the program and then get the error.
I think I may have misunderstood the documentation, can someone please
suggest how to perform this analysis correctly?!

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