Hi Reza,
RMSF is the way that you can measure the fluctuation of each residue.
Best regards
Homa
> Hello all,
>
> I ran a 10ns MD simulation with a protein containing 181
> aa and I want to
> obtain average value of RMSd for each
> residue (or alpha carbons) during the last 5ns and then
> plot it against the
> residue number.
>
> How is it possible to plot RMSd of a protein versus residue
> number with
> ptraj? what else could be done to obtain such plot?
>
> Ragards,
> M. Reza
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Received on Mon May 31 2010 - 17:00:05 PDT
