[gmx-users] fluctuation of protein coordinates

Lars Schaefer 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..

use g_rmsf

also i
> want to visualise the drift of protein structure from
> the initial model..

use g_rms

> Can anyone tell me how to do so? 
> It will be greatly appreciated.
> Thanks in advance
> shailza.

note that 1ns is really quite short - or is it just a test / equilibration?
Cheers, Lars

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