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...>
 >
 >
 > --
 > gmx-users mailing list gmx-users@gromacs.org
 > http://lists.gromacs.org/mailman/listinfo/gmx-users
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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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