[gmx-users] g_rmsf reference structure?

kulleperuma.kulleperuma at utoronto.ca kulleperuma.kulleperuma at utoronto.ca
Wed Feb 16 05:44:59 CET 2011

Dear all,

I use g_rmsf of Gromacs VERSION 4.0.5 to calculate the RMSF of the  
C-atoms with reference to the average structure between 5-10 ns of a  
total of 10 ns simulation as below;
g_rmsf  ?f md.xtc  ?s md.tpr ?b 5000 ?e 10000 ?o rmsf.xvg

My understanding of the RMSF is as follows;

  RMSF = sqrt( 1/T ?[(xi(t)-Xi)]^2)

where T is the time over which one wants to average, and Xi is the  
reference position of particle i, which is the time-averaged position  
of the same particle i.
What I am confused is whether g_rmsf takes the reference structure  
from the structure file (-s), which in my case, the md.tpr and NOT the  
time averaged position over the specified time?

Thanking in advance for clarification.

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