[gmx-users] Re: help me with g_rmsf...

[mekanix]

Hi Tsjerk!
Thx very much for the help!!!!
It's been very helpfull!! 

 


Hi Rodolfo, 

With regards to the first question, the difference is that for the RMSF, you
first determine the average position for each particle and then calculate
the deviation from the average for every time frame, summing the square of
the result and dividing by the number of frames. When using -od, instead of
taking the deviation from the average position, the deviation from the
reference position is taken. In that case the deviations will be larger in
general and the result is heavily dependent on the choice of the reference.
For the most useful results, use -o rather than -od. 

The difference between g_rms and g_rmsf is basically that with g_rmsf you
average over time, getting atom or residue specific values, whereas with
g_rms you average over atoms, getting time specific values. 

Hope it helps, 

Tsjerk