[gmx-users] Potential Energy Landscape

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 12 19:22:21 CEST 2011

Natalie Stephenson wrote:
> I was recently told in passing that it would be possible to construct a 
> 'potential energy landscape' from the simulations I have performed.  
> This way I could remove any loading rate differences between simulations 
> and experimental force experiments I've been performing ... however I 
> cannot find anywhere in which this is mentioned.
> The only thing close I could find that was close was the free energy 
> landscape using g_anaeig under the Dihedral PCA 
> (http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca 
> <http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca>) 
> however, I'm not sure this is what I'm looking for. 
> Does anyone know where I would be able to find out / read more about how 
> to create potential energy landscapes from my simulation outputs?

g_sham produces free energy landscapes for any variables plotted against one 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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