# Re: [AMBER] How to combine RMSF profiles?

Date: Thu, 30 Aug 2012 11:10:43 +0800

Dear Jason,
Could you mind to teach me how to extract every 5th snapshot with cpptraj?
If I have a total of 1 to 500 frame in xxx.mdcrd, is it correct?
trainin xxx.mdcrd 1 500 5
Best regards,
Catherine

> Date: Wed, 29 Aug 2012 10:38:46 -0400
> From: jason.swails.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] How to combine RMSF profiles?
>
> On Wed, Aug 29, 2012 at 1:49 AM, Catein Catherine <askamber23.hotmail.com>wrote:
>
> >
> > I was trying to calculate the RMSF for a trajectory. Since it is a long
> > trajectory (1000 ns), I cannot do the cpptraj analysis in one-goes with
> > supercomputer with only 24G RAM. I have to do it step by step. However,
> > I have a problem, if I want to plot RMSF (per residues) vs residue number
> > for the whole trajectory, for instance if I got three profiles 1-300 ns,
> > 301 to 600 ns and 601 to 1000 ns. What should I do to combine all the
> > three profile into one single profile that represent the whole trajectory?
> >
>
> Look at the RMS formula ( sqrt( sum(x^2) / N) ) and try to combine each
> section such that the formula you use is ultimately equivalent to the
> formula for the RMSF of the entire trajectory.
>
> So for instance, for each data point, square the RMSF value, multiply by
> the number of frames in that window (this value should be equal to sum(x^2)
> now), then add up for all 3 windows. Then divide by the total number N
> over all 1000ns and take the square root to arrive back at the RMSF formula
> for the whole trajectory.
>
> You could also try extracting every 5th snapshot from the original
> trajectory and performing the whole analysis in one run.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Wed Aug 29 2012 - 20:30:02 PDT
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