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-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Natalie Stephenson [natalie.stephen...@postgrad.manchester.ac.uk]
Sent: 14 November 2011 12:15
To: jalem...@vt.edu; Discussion list for GROMACS users
Subject: RE: [gmx-users] Potential Energy Landscape
________________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@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-boun...@gromacs.org
[gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul
[jalem...@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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