[gmx-users] g_rmsf, mass-weighted residue average

[Leandro Bortot]

Dear users,

     I'm doing some RMSF analysis of my simulations and I came across
something I can't understand. Any help is greatly appreciated.

     I got the all-atom RMSF and manually calculated the mass-averaged
residue RMSF values, but they are not equal to those given when using -res
with the very same trajectories (-f), references (-s), times (-b, -e and
-dt) and index file (Protein). I used the atom masses as given in the
topology.

     I tried to check the source (gmx_rmsf.c), and according to what I
understood the procedure is indeed to mass average pre-calculated atomic
rmsf values. Is there anything I'm missing?


Thank you for your attention,
Leandro.