[gmx-users] Potential Energy Landscape

Natalie Stephenson Natalie.Stephenson at postgrad.manchester.ac.uk
Fri Oct 21 11:48:57 CEST 2011

Hi Justin (and gmx-users),

I've been looking into using g_sham for the free energy landscapes, however I'm not sure what variables I should plot ... could I just use the g_energy (potential) outputs to produce the energy landscape??  Other examples I've seen using g_sham have done quite in depth eigenvector projections before plotting them using g_sham.

What inputs would I require in order to determine how loading rate an increased loading rate on the simulation would change the force results?

I know I'm probably being completely dumb but my use of maths has been sporadic to say the least in the last 7 years ... so getting back into it is proving more confusing!


Natalie Stephenson, B.Sc
PhD Research Associate

Manchester Interdisciplinary Biocentre
131 Princess Street
M1 7DN

From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
Sent: 12 October 2011 18:22
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Potential Energy Landscape

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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