[gmx-users] g_rmsf over time windows

giordano mancini baloilgiullare at interfree.it
Wed Oct 8 13:02:51 CEST 2008

Hi Tsjerk,

thanks for your reply.
I have inspected a trajectory
movie with vmd and made a superimposition of the starting and last
configuration with the reference structure (which is just the the
crystallographic pdb) and (inspecting them visually),
I do not see any significant conformational change (apart in one 
subdomain,but this is expected). I agree that 10 ns
are a short sampling but the total simulation time is 15 ns + 2 ns I
used to reach 298K; since the rmsd was almost flat in this 10 ns I was
hoping that results were not influenced by relaxation.
Maybe g_rmsf calculates fluctuations from the average structure in a 
certain time window and not from the reference or starting frame
(and it is my fault not to have read the program help well). In this 
case my results would make sense.


Tsjerk Wassenaar wrote:
> Hi Giordano,
> Do you have a conformational change? If you consider unidirectional
> motion, in one or N coordinates alike, you would expect just what you
> see for the fluctuations. In fact, it's not really fluctuation then.
> 10 ns is also pretty short for a simulation of a protein. It's likely
> that you're analyzing relaxation from the starting structure.
> Cheers,
> Tsjerk

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