[gmx-users] large error bars in PMF

Rebeca García Fandiño regafan at hotmail.com
Fri Jul 22 14:41:34 CEST 2011

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,

> Date: Fri, 22 Jul 2011 08:23:18 -0400
> From: chris.neale at utoronto.ca
> To: gmx-users at 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.neale at 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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