[gmx-users] Potential Energy Landscape

[Justin A. Lemkul]

Natalie Stephenson wrote:
> 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.
> 

The free energy of potential energy is probably not a meaningful quantity ;)

> 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!
> 

You haven't provided a lot of detail about what you're doing, what you've 
measured, or what you hope to achieve.  In general, one plots two variables (one 
on each axis), and g_sham calculates a free energy based simply on the 
probability of occurrence of these values.  For instance, for protein folding 
experiments, often the RMSD relative to the known structure is one variable, and 
something else like native contacts or hydrogen bonds is plotted as the other 
variable.  The free energy surface is then generated as a function of 
intramolecular association and similarity to a known structure.

-Justin

> Natalie
> 
> ------------------------------------------------ Natalie Stephenson, B.Sc PhD
> Research Associate
> 
> Manchester Interdisciplinary Biocentre 131 Princess Street Manchester M1 7DN 
> x65816 ------------------------------------------------
> 
> ________________________________________ 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 
> 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
> 
> ======================================== -- gmx-users mailing list
> gmx-users at gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please
> don't post (un)subscribe requests to the list. Use the www interface or send
> it to gmx-users-request at gromacs.org. Can't post? Read
> http://www.gromacs.org/Support/Mailing_Lists

-- 
========================================

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

========================================