On 12/30/12 12:28 PM, Nash, Anthony wrote:
Dear gmx users,
I posted a couple of weeks ago with regards to correctly using umbrella
sampling and the WHAM on atomistic transmembrane proteins with a reaction
coordinate as a function of interhelical distance. I have a single TM dimer,
but with a different transmembrane domain face at the helix-helix interface.
So you have proteins with identical sequences in each case, but different
orientations?
What did I conclude from the replies? Correct calculation of the differences
in free energy is taken by normalizing to zero at the plateau (flat) of the
graph i.e., where your PMF graph (after g_wham) flattens out you apply the
-zprof0 at this point, before calculating the difference between of each
system.
The problem I face is that this occurs around 6.8 - 7.5nm along the reaction
coordinate. And, applying a umbrella window every half angstrom has made this
extremely computationally expensive. However, I have persisted, and I have
Every half Angstrom? That sounds like massive overkill for almost any system.
Do you mean half nanometer instead?
all my graphs, and I have a plateau on all of them. Yet the PMF graphs
between 4 - 7.5 nm are not yet converging or close to the same sampled
energy, even though all four systems are identical in amino acid composition.
Each window has ran for up to 40 ns.
Are there any differences at all in these systems, or are they simply intended
to be replicates of one another? I'm just curious to know what you're comparing
here.
So when I normalise, depending on where I normalise I will get massively
different difference in free energies.
Real numbers would help us understand what's going on here, as would a report of
the error estimate that g_wham cna provide.
I have tried the strategy of taking the windows of a particular systems at
4.5 nm to 7.5 nm along the reaction coordinate (where there is no short range
interaction), and applying those windows into the other three systems. This
brings their region of plateau a lot closer together, whilst preserving the
windows and the convergence of the region along the reaction coordinate where
there are close-range forces in play (converges 0.8 nm - 4.5 nm).
Alternatively, could I make the assumption that as their amino acid
composition is identical across all four systems, I can normalise where each
of the four graphs finish converging (around 4.5 nm)?
In theory, two peptides that are at a given distance from one another can sample
basically an infinite number of configurations, so at some point you should see
some similarities between the different systems. During the length of a 40-ns
MD simulation, such an assumption likely is not valid, so picking and choosing
configurations that you think will make the results better is questionable, at
best. Since you're dealing with a lipid bilayer, you can't consider only the
protein dynamics; you have lipid reorientation times that may be at play,
especially in the presence of artificial restraints between the proteins. There
is an interplay between all elements of the system, and 40 ns may not be long
enough to assure that you really have sufficient sampling (heartbreaking to
hear, I know, especially for expensive simulations like umbrella sampling).
On a related note, how large are your boxes? Is there adequate space between
periodic images at such a large COM separation? I would imagine that your
systems would have to be quite large to avoid spurious PBC interactions. Are
you pulling along a single dimension or along a diagonal? Can you post any
images to demonstrate two systems that give very different results, but visually
seem that they should not? There is so much to guess at here that it's very
difficult to make conclusive recommendations.
I would really appreciate any advice from someone who has insight on this
issue. I have looked through many journals and founds lots of entries where
they just stop at 2.0 nm with no plateau, yet I haven't found a single WHAM
of reconstructing umbrella windows where they normalise at the plateau. I
Shameless plug:
http://pubs.acs.org/doi/abs/10.1021/jp9110794
have also contacted a few authors of journals with regards to why they cut
off at 2 nm. None of them took into consideration that their PMF graphs were
still raising.
Typical ;) There are a fair number of very questionable PMF curves in the
literature, I'm afraid.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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