Rebeca García Fandiño wrote:
Hello,
some days ago you had recomended me to use a dodecahedron box and
"pull_dim = Y Y Y" to try to decrease some error bars I was obtaining
in my PMF calculations (trying to calculate the binding energy of two
cyclic peptides).
Now, I have run these calaculations, but I have a doubt for the analysis.
How should I analyze the results, using g_wham like in the case of
"pull_dim = N N Y". I have not seen any option in g_wham to indicate
this is a 3D PMF. I have also seen in this list these days that 3D-Wham
was recomended (for a case different to mine).
So, how should analyze the results obtaind from "pull_dim = Y Y Y" ?
Just as you would previously.
-Justin
Thanks a lot for your help.
Best wishes,
Rebeca.
------------------------------------------------------------------------
From: rega...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] large error bars in PMF
Date: Fri, 22 Jul 2011 12:41:34 +0000
I have used a cubic box of dimensions 8 x 8 x 14 (nm), and my total
pulling was 5nm along the z direction. I dont´t think there could be a
problem with the PBC, since the layer of solvent around the protein is
quite big, although I suppose that using a dodecahedron box for this
system would have been better.
I will try now the "pull_dim = Y Y Y" and see what it happens.
Thanks a lot for the suggestions!
Best wishes,
Rebeca.
> Date: Fri, 22 Jul 2011 08:23:18 -0400
> From: chris.ne...@utoronto.ca
> To: gmx-users@gromacs.org
> Subject: [gmx-users] large error bars in PMF
>
> I see now what you mean. As it happens, I doubt that this would have
> caused the problem since no force was applied on X and Y dimensions,
> so it would require that there was a PBC-based distance degeneracy
> along Z, although this is of course possible and hopefully Rebecca
> will answer this part.
>
> Also, thanks for the pull_dimension/pull_vec fix.
>
> Chris.
>
> -- original message --
>
>
> chris.ne...@utoronto.ca wrote:
>
> [Hide Quoted Text]
> I don't see why the box-type makes any difference whatsoever. It is
> possible that if you use a rhombic dodecahedron, you may reduce the
> system size, thus simulate more ns/day, thus converge faster, but that
> should be the only effect. I would be interested to hear more from
> Justin about how the box-shape is expected to affect peptide rotation...
> perhaps I misunderstand this point.
> My point was not that the box shape has any effect on protein
rotation. That
> will happen regardless of the box shape, of course. My suggestion for
> this box
> type was that since Rebeca has a system that is essentially spherically
> symmetric (i.e. two proteins connected by some arbitrary vector,
which are at
> the same time rotating freely), then she must use a suitable box
shape that
> reflects this type of symmetry. I never got a clear answer to whether
or not
> the weird interactions she cited were due to PBC or not, but if one
uses a
> rectangular box for a system like this one, there can be artificial
> interactions
> very easily.
>
> [Hide Quoted Text]
> I have a few other comments.
>
> 1. If you allow the peptide to rotate freely, then you do indeed need to
> converge all of their different rotational interactions. An alternative
> is to apply orientational restraints during the pulling (assuming that
> you know the bound state) and then to correct to an unrestrained state
> at large separations. You can see, for instance, D. L. Mobley, J. D.
> Chodera, K. A. Dill. "On the use of orientational restraints and
> symmetry number corrections in alchemical free energy calculations", ...
>
> 2. You are using "pull_dim = N N Y" which, if I haven't entirely
> forgotten how the pull-code works, means that the distance along Z is
> restrained but the distance along X and Y is free to change. What you
> end up with by sampling in this way is pretty strange and will require a
> really weird volumetric correction in the absence of infinite sampling
> time. You must decide to either: (i) pull to a spherical distance:
>
> pull_dim = Y Y Y
> pull_geometry = distance
>
> or (ii) to pull along a defined vector
>
> pull_dim = Y Y Y
> pull_geometry = direction
> Just a note here - if you set direction geometry, the pull_dim
keyword is not
> used, but pull_vec is.
>
> -Justin
>
> [Hide Quoted Text]
> What you have done:
>
> pull_dim = N N Y
> pull_geometry = distance
>
> is only really useful when the system is isotropic along the XY plane
> (at least in the time averaged sense), such as for a lipid bilayer, or
> when the freedom in X and Y is very low, such as in a channel.
>
> 3. Finally, just because you sampled *more* doesn't mean that your
> values are converged. Look into block averaging and test to see if your
> binding free energy is drifting over time.
>
> Good luck,
> Chris.
>
> -- original message --
>
> Hi again,
> I have one doub about the suggestion of using a dodecahedral box for my
> umbrella sampling to remove the problems I am having with the peptides
> rotating. I cannot see why a dodecaheral box is going to avoid this.
> Would it be better a truncated octahedron?
> Thanks a lot for your help.
> Best wishes,
> Rebeca.
>
> <... snip...>
>
>
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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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