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

Leandro Bortot leandro.obt at gmail.com
Thu May 7 06:52:26 CEST 2015

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

     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,

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