Re: [AMBER] Free Energy Landscape for cMD Help

From: Jason Swails <>
Date: Wed, 17 Jun 2015 22:26:18 -0600

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

> I am trying to calculate Free energy landscape for my bound and unbound
> protein species using following script. I have read plenty of AMBER thread
> on this but does not seems to get an hold this. Please let me know if this
> is a right way of calculating free energy landscape for classical dynamics.
> Thanks
> in advance.
> ptraj .filename.prmtop <<EOF6 > filename-run6.out
> trajin filename.mdcrd.gz 1 49000 1
> reference reference.pdb
> rms reference .CA mass
> projection modes filename-pca100vec.dat out filename_1-10.dat beg 1 end 10
> .CA
> EOF6
> After copying first two PCA modes in to pca12-ca file
> #
> readdata pca12-ca
> 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

Long answer: this is a potential of mean force using the first two
principal components as the collective variables. You would have to look
at the corresponding eigenvectors of these modes (or generate
pseudo-trajectories of various projections along these modes) in order to
get an understanding of the types of motions that these collective
variables describe.

Short answer: yes, this is a way of computing a free energy landscape from
MD results.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Jun 17 2015 - 21:30:03 PDT
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