[gmx-users] Potential Energy Landscape

Natalie Stephenson Natalie.Stephenson at postgrad.manchester.ac.uk
Tue Nov 29 10:54:56 CET 2011 

Thanks I'll give PCA a try! 

Natalie


________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Mark Abraham [Mark.Abraham at anu.edu.au]
Sent: 21 November 2011 12:04
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Potential Energy Landscape

On 21/11/2011 10:36 PM, Natalie Stephenson wrote:
> I have performed force pulling experiments on a protein with both Gromacs MD simulations and experimentally with AFM.  The problem I'm facing with the data is the difference between the loading rates of the two approaches.  For the MDS the loading rate is around 10 N/s, whereas the AFM experiments have a much lower loading rate of 1 x 10^-8 N/s.
>
> I was told at a conference I attended that there was a way of constructing a 'potential energy landscape' which would be able to use this to remove the loading rate differences. However, I did not get a chance to find out how this was possible.  I understand how g_sham works, however, I'm not sure what - in this case - the input would be in order to construct such a 'potential energy landscape'. Any insight into how I would be able to create this ... or any other ideas on how I would be able to somehow relate the simulation output to experimental data dispite the loading rate differences would be GREATLY appreciated!!

Forget the misleading term "potential energy landscape". It seems nobody
here knows how your contact thinks constructing a plot of free energy as
a function of two observables will address the loading rate difference.
Justin described how g_sham works. Your analysis may suggest the right
observables for use with g_sham, or you may wish to use essential
dynamics (aka principal component analysis) to determine these
algorithmically. Check out manual 8.10 if so.

Mark

>
> Thanks once again!!
> 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 Natalie Stephenson [Natalie.Stephenson at postgrad.manchester.ac.uk]
> Sent: 14 November 2011 12:15
> To: jalemkul at vt.edu; Discussion list for GROMACS users
> Subject: RE: [gmx-users] Potential Energy Landscape
>
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
> Sent: 21 October 2011 13:25
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Potential Energy Landscape
>
> 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
>>
> Sorry it's taken so long to reply to this one, experimental issues dragged my focus!
> I have performed force pulling experiments on a protein with both Gromacs MD simulations and experimentally with AFM.  The problem I'm facing with the data is the difference between the loading rates of the two approaches.  For the MDS the loading rate is around 10 N/s, whereas the AFM experiments have a much lower loading rate of 1 x 10^-8 N/s.
>
> I was told at a conference I attended that there was a way of constructing a 'potential energy landscape' which would be able to use this to remove the loading rate differences. However, I did not get a chance to find out how this was possible.  I understand how g_sham works, however, I'm not sure what - in this case - the input would be in order to construct such a 'potential energy landscape'. Any insight into how I would be able to create this ... or any other ideas on how I would be able to somehow relate the simulation output to experimental data dispite the loading rate differences would be GREATLY appreciated!!
>
> Thanks once again!!
> Natalie
>
>> 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
>>
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> --
> ========================================
>
> 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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