Hi 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?!
Thanks Jo
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