On 16/02/2011 3:44 PM, [email protected] 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.
Mark
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