Re: [AMBER] Free Energy Landscape for cMD Help

From: Daniel Roe <>
Date: Thu, 18 Jun 2015 09:16:07 -0600


On Wed, Jun 17, 2015 at 8:17 PM, bharat lakhani <>

> runanalysis hist pca12-ca1:1 pca12-ca1:2 free 300 out fhist-all.gnu bins
> 400
> Then plotting 3D free energy plot from fhist-all.gnu

Be very careful using the term "free energy" here. This kind of calculation
assumes that you have good sampling of the underlying distribution of
conformations. Unless you can show that you have good sampling, you cannot
really call this a free energy - at best it becomes a logarithmic-weighted
population histogram. In my opinion you need to have at least one other
independent simulation (ideally from a different initial conformation) and
show that the populations from the second simulation converge with those
from the first before you can even think about talking free energy. For
some examples of the types of analysis you can do to ascertain convergence
see and (although the simulations are
REMD the same analysis can apply to MD). Also note that these examples are
by no means the only way to check convergence.


PS - FYI the above two scripts could be consolidated into one with cpptraj:

readdata filename-pca100vec.dat name MyEvecs
parm filename.prmtop
trajin filename.mdcrd.gz 1 49000
reference reference.pdb
rms reference .CA mass
projection MyProjection evecs MyEvecs out filename_1-10.dat beg 1 end 10
hist MyProjection:1 MyProjection:2 free 300 out fhist-all.gnu bins 400

> --
> regards
> Bharat Lakhani
> _______________________________________________
> 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 Thu Jun 18 2015 - 08:30:03 PDT
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