Re: [AMBER] aMD plot

From: Daniel Roe <>
Date: Tue, 6 Jan 2015 21:34:59 -0700


I'm glad the input I gave you worked, however since your data is from
accelerated MD you do have to reweight it (assuming you want the
unbiased surface) which I forgot to say previously as Thomas pointed
out. You can do this by using the 'amd <dataset>' keyword with the
'hist' command, where <dataset> is a previously read in data set (with
aMD boost values in KT). For example:

readdata pca12-ca
readdata amdboost
runanalysis hist pca12-ca:2 pca12-ca:3 free 300 \
  out fhist.gnu bins 400 amd amdboost

Note this is just a straight reweight. I think that the scripts Thomas
pointed you to use a kernel density estimator to smooth things out a
bit and so usually end up with nicer-looking plots so it may be
worthwhile to play around with them some more.


PS - Keep in mind that reweighting aMD data via boost energies can be
somewhat difficult and noisy, particularly if the boost values are
large (see e.g. for an
explanation of why this is). I think if your boost energies are
relatively small things should be ok.

On Tue, Jan 6, 2015 at 5:48 PM, 汪盛 <> wrote:
> First of all, thanks Daniel Roe very much.
> Actually the cpptraj input lines provided by Daniel Roe works very well.
> In addition, if one like, the matplotlib may also plot a very beautifull aMD "free energy"plot for you.
> I hope that these cpptraj input lines can be added to the formal Amber tutorials-A22 sections 3, these can help others to understand the aMD quickly.
> _______________________________________________
> 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 Tue Jan 06 2015 - 21:00:02 PST
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