Re: [AMBER] PCA_representation_in_Cpptraj

From: Daniel Roe <>
Date: Wed, 11 Mar 2015 08:25:57 -0600


On Wed, Mar 11, 2015 at 6:52 AM, Juan Eiros Zamora
<> wrote:
> Is there any way I can use the KDE to calculate the Free Energy in the
> PCA 2D plot? Looking in the Amber manual I've found that the only option

No, multivariate KDE is actually a different beast than single
variable KDE and is not yet implemented in cpptraj. However, choosing
bin sizes for histograms really isn't that big a deal; just make sure
you choose enough bins that you get decent resolution. For example, if
my PC covers a spread of 80 Angstroms, 200 bins will provide good
resolution (0.4 Ang step size) and assuming I am binning much more
than 200 points (say 50k) the resulting histogram won't be too sparse.
Alternative, you could specify a step size instead of the number of
bins (with 'step').


> for the hist command is with bins. Or a way where I could do the 1D
> histogram with kde command and then transfer it to the PCA projection
> file? I think it would be a better idea than selecting myself the bin
> size, as Jason mentioned that it is a better solution for this problem.
> Thank you for your time,
> Juan
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Mar 11 2015 - 07:30:03 PDT
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