[gmx-users] g_rmsf reference structure?

Mark Abraham Mark.Abraham at anu.edu.au
Wed Feb 16 07:08:33 CET 2011

On 16/02/2011 3:44 PM, kulleperuma.kulleperuma at utoronto.ca wrote:
> 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?

It does take the reference structure from -s. Whether you actually want 
the RMSF from the non-physical time-averaged structure is up to you. 
IIRC you might be able to get such an average from g_cluster.


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