[gmx-users] The rmsf -res option

Laura Tociu ltociu at princeton.edu
Sun Dec 13 19:39:20 CET 2015

Dear Gromacs users,

I ran two commands:

gmx rmsf -s protein_1_block_1_reference.gro -f protein_1_traj.xtc -o
residues_protein_1_block1.xvg -b 0 -e 40000 -res


gmx rmsf -s protein_1_block_1_reference.gro -f protein_1_traj.xtc -o
protein_1_block_1.xvg -b 0 -e 40000

and selected Protein-H for the output group.

I am trying to figure out if -res computes the MSF by mass-averaging or
just a usual average. I tried to calculate the MSF of the first residue
myself from protein_1_block_1.xvg, but neither a simple average nor a
mass-average gave the exact number I got with the -res option. The numbers
were close but not exactly the same.

Can someone please help me understand how -res works?  Maybe with a
formula, I might be doing it wrong.



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