Re: [AMBER] How to combine RMSF profiles?

From: Carlos Simmerling <>
Date: Wed, 29 Aug 2012 10:48:11 -0400

Thinking of just combining them misses some value. Analysis should always
contain precision estimates. I suggest doing 2 pieces if possible, then
reporting the average and using the 2 values to indicate error bars. Of
course this is a simplistic approach to uncertainty estimation, but it's
easy given what you already did.
On Aug 29, 2012 1:49 AM, "Catein Catherine" <> wrote:

> Dear Sir/Madam,
> 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?
> Best regards,
> Catherine
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Received on Wed Aug 29 2012 - 08:00:05 PDT
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