[gmx-users] RMSF calculations

Gurunath Katagi gurukatagi at gmail.com
Mon Oct 10 12:22:50 CEST 2011

Dear all,
I have a set of proteins(in pdb format) in which some are solved by X-ray
diffraction and some by NMR.
I have done the md simulation of these proteins using gromacs for 30ns [For
NMR structures, i have taken the first model as the starting structure]

Now, that i want to calculate the RMSF value from the simulations and
compare with the RMSF values from experimental structures [X-ray/NMR]
For the proteins with crystal structures , calculation is done using using
g_rmsf function and the comparison is done.

and  for protein from NMR structure , the RMSF values are calculated from
the simulation trajectory. But in order to compare these, how does one get
the RMSF values ? ,since
 the pdb file doesn't have the b-factors ..

Is it a good idea to use the  NMR ensembles ( usually 20 models from NMR) to
derive the RMSF  and compare these with simulation results ..?
or is there any other parameter that i can calculate from NMR models, which
is similar to RMSF ..?

Thanksin advance ..

Thanking You
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