Hi,
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.
-Dan
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.
http://www.ncbi.nlm.nih.gov/pubmed/22015376 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 <shengwang.hust.edu.cn> 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.
> _______________________________________________
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> 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)
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Received on Tue Jan 06 2015 - 21:00:02 PST
