Thanks Erik! /PK
2012/11/16 Erik Marklund <er...@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 > > about this. It is a global atom number > > 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 > > affect your results. > > > > Chris. > > -- > > 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? Read http://www.gromacs.org/Support/Mailing_Lists > > ----------------------------------------------- > 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 > er...@xray.bmc.uu.se > http://www2.icm.uu.se/molbio/elflab/index.html > > -- > 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? Read http://www.gromacs.org/Support/Mailing_Lists > -- 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? Read http://www.gromacs.org/Support/Mailing_Lists