# [gmx-users] Re: Umbrella sampling question

Gmx QA gmxquestions at gmail.com
Fri Nov 16 16:41:45 CET 2012

```Thanks Erik!

/PK

2012/11/16 Erik Marklund <erikm at xray.bmc.uu.se>

> Hi,
>
> Blindly defining the center of mass for a group of atoms is not possible
> in a periodic system such as a typical simulation box. You need some clue
> as to which periodic copy of every atom that is to be chosen. By providing
> pull_pbcatom0 you tell gromacs to, for every atom in grp0, use the periodic
> copy closest to the atom given by pull_pbcatom0. If you have large
> pullgroups this is necessary to define the inter-group distance in a way
> that makes sense. If you get different results depending on that setting
> you really need to figure out which atom is a good center for your
> calculations. The default behavior is to use the atom whose *index* is in
> the center of the group. If you for example have a dimeric protein this may
> correspond to the C-terminus of the first chain or the N-terminus of the
> second one, which in turn often doesn't coincide with the geometrical
> center of the group. I suggest you try yet another choice of pull_pbcatom0
> that is also close to the center to see if that also give rise to a
> different distance. As mentioned, the choice of pull_pbcatom0 should not
> matter as long as the choice allows to figure out how to handle the
> periodicity.
>
> Best,
>
> Erik
>
> 15 nov 2012 kl. 19.56 skrev Gmx QA:
>
> > Hi Chris
> >
> > Seems my confusion was that I assumed that the distances in the
> > profile.xvg-file should correspond to something I could measure with
> > g_dist. Turns out it does not.
> > Thank you for helping me sorting out this, I got it now :-)
> >
> > About pull_pbcatom0 though. My box is >> 2*1.08 nm in all directions:
> > \$ tail -n 1 conf0.gro
> >  12.45770  12.45770  17.99590
> >
> > I am still not sure what pull_pbcatom0 does. You said it should not have
> > any effect on my results, but changing it does result in a different
> > initial distance reported by grompp.
> >
> > In my initial attempts at this, I did not specify anything for
> > pull_pbcatom0, but in the grompp output I get this
> >
> > Pull group  natoms  pbc atom  distance at start     reference at t=0
> >       0     21939     10970
> >       1         1         0   2.083                 2.083
> > Estimate for the relative computational load of the PME mesh part: 0.10
> > This run will generate roughly 761 Mb of data
> >
> >
> > Then, following the advice in the thread I referred to earlier, I set
> > pull_pbcatom0 explicitly in the mdp-file to be an atom close to the COM
> of
> > the Protein. Then I get from grompp
> >
> > Pull group  natoms  pbc atom  distance at start     reference at t=0
> >       0     21939      7058
> >       1         1         0   1.808                 1.808
> > Estimate for the relative computational load of the PME mesh part: 0.10
> > This run will generate roughly 761 Mb of data
> >
> > As you can see, the initial distance is different (2.083 vs 1.808), and
> > 1.808 is the same as the distance reported by g_dist. Do you have any
> > comments here as to why this is?
> >
> > Thanks
> > /PK
> >
> >
> > What you reported is not what you did. It appears that grompp, gtraj, and
> > g_dist report the same value.
> > Please also report the value that you get from your pullx.xvg file that
> you
> > get from mdrun, which I suspect
> > will also be the same.
> >
> > The difference that you report is actually between the first FRAME of
> your
> > trajectory from g_dist
> > and the first LINE of the file from the g_wham output. I see no reason to
> > assume that the values in the
> > output of g_wham must be time-ordered. Also, I have never used g_wham
> > myself (I use an external program
> > to do wham) and so I can not say if you are using it correctly.
> >
> > My overall conclusion is that you need to investigate g_wham output not
> > worry about a new run at this stage.
> >
> > Regarding pull_pbcatom0, there is lots of information on the mailing list
> > that defines the unit cell for selection of which periodic image of each
> > molecule will be used for the pulling.
> > If all of your box dimensions are >> 2*1.08 nm, then pull_pbcatom0 will
> not
> >
> > Chris.
> > --
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>
> -----------------------------------------------
> Erik Marklund, PhD
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 6688        fax: +46 18 511 755
> erikm at xray.bmc.uu.se
> http://www2.icm.uu.se/molbio/elflab/index.html
>
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```