[gmx-users] fluctuation of protein coordinates
Lars.Schaefer at mpi-bpc.mpg.de
Sat Feb 26 12:16:11 CET 2005
shailza singh wrote:
> hi all,
> i am using GROMACS-3.2.1 and ran simulation of my
> protein for 1ns..i want to calculate the RMSF's of the
> C-alpha coordinates from their time averaged
> values(last 200-ps simulation) as a function of
> residue number but not being able to do so..
> want to visualise the drift of protein structure from
> the initial model..
> Can anyone tell me how to do so?
> It will be greatly appreciated.
> Thanks in advance
note that 1ns is really quite short - or is it just a test / equilibration?
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