Hi,
On Wed, Mar 11, 2015 at 6:52 AM, Juan Eiros Zamora
<j.eiros-zamora14.imperial.ac.uk> 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').
-Dan
> 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
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 11 2015 - 07:30:03 PDT
