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" ? 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 > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? 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