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
another.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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