Re: [gmx-users] G_rmsf, reference structure

Hi Floris, By default it's A. There is an option for doing B. But B makes no sense. Cheers, Tsjerk On Apr 3, 2015 1:10 PM, Eerden, van, F.J. f.j.van.eer...@rug.nl wrote: Dears, I have calculated the RMSF from a protein trajectory in Gromacs 4.5.5. My question is how the RMSF is

[gmx-users] G_rmsf, reference structure

Dears, I have calculated the RMSF from a protein trajectory in Gromacs 4.5.5. My question is how the RMSF is calculated: A) 1) fitting of the trajectory to the tpr file supplied by -s 2) calculating the averaged atom coordinates over time (x~) 3) calculating the deviation from the averaged