Hi Paul, Thanks for this idea --
...But it returns what I would expect: Statistics over 1 steps [ 200000.0000 through 200000.0000 ps ], 3 data sets All statistics are over 1 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Box-X 12.2482 -- 0 0 (nm) Box-Y 12.2482 -- 0 0 (nm) Box-Z 12.2482 -- 0 0 (nm) This matches what the pdb extracted file says (i.e. the file which does not have the complex centered at the Box-X/2, Box-Y/x, Box-Z/2) So I'm still not sure what's going on -- any other thoughts? Mala On Fri, Feb 8, 2019 at 5:39 AM Peter Kroon <p.c.kr...@rug.nl> wrote: > What does "gmx energy -b 20000 -e 20000" give as box dimensions? > > > Peter > > On 07-02-19 22:20, Mala L Radhakrishnan wrote: > > Hi Justin, > > > > Thank you -- the good news is that the center of mass of this group does > in > > fact match what I calculate to be the COM with my script. > > > > BUT, the bad news is that this is not in the center of the box after I > have > > asked for it to be centered (which I presume it should be):: > > > > COM: > > 5.95324 6.00572 5.68943 > > > > The cubic box is 12.249 long (as noted in the CRYST1 field of the pdb > file > > and its left corner is at the origin (I know this because I have atoms > that > > go all the way to the edges of the box and my minimum x,y, and x > > coordinates are basically 0 and my maximum are basically 12.24 in all > three > > directions, which would make the center of the box: > > > > 6.1245, 6.1245, 6.1245 > > > > So it's close but a few angstroms off. Can you please tell me what might > > be going on here? I am happy to share files with, as I'd be really > > grateful for your help. Again, I've written a scrip to translate and > > "wrap" the atoms across the pbc in the worst case scenario, but I have to > > imagine gromacs should be able to do this correctly. > > > > Again - this is the command I used to extract the hopefully centered > frame: > > gmx trjconv -f md.xtc -o all.pdb -s md.tpr -b 200000 -e 200000 -n > INDEX.ndx > > -pbc atom -center > > > > ...and I chose the correct index (and extracted the same atoms just in > case > > to make sure that I knew exactly what atoms it thought it was centering, > in > > case something was in fact wrong with the index file) > > > > Thank you so much, > > > > Mala > > > > > > On Thu, Feb 7, 2019 at 1:54 PM Justin Lemkul <jalem...@vt.edu> wrote: > > > >> > >> On 2/7/19 1:52 PM, Mala L Radhakrishnan wrote: > >>> Hi Justin, > >>> > >>> I've verified the I'm entering in the right group and that it's correct > >> in > >>> the index file. Where do I find the output for what it thinks is the > >>> center of mass before and after? That would be helpful output, but I > >>> haven't found such output in standard output or error. > >> gmx traj -ox -com > >> > >> -Justin > >> > >>> thanks again for instructions on how to get this info.. > >>> Mala > >>> > >>> On Thu, Feb 7, 2019 at 1:46 PM Justin Lemkul <jalem...@vt.edu> wrote: > >>> > >>>> On 2/7/19 1:36 PM, Mala L Radhakrishnan wrote: > >>>>> Thanks...but these don't really address the issue I have. I've > written > >>>> my > >>>>> own script now to do re-centering and looping of atoms across the box > >>>> walls > >>>>> myself, but I am still really unclear why -center does not in fact > >> center > >>>>> the molecule in the box either at its geometric center OR its center > of > >>>>> mass (I have written scripts to test both out and neither match, and > >>>>> visually the molecule is clearly not centered in the box) > >>>>> > >>>>> To me it definitely seems like something is not right with this > utility > >>>> or > >>>>> something about the options I've used are conflicting in ways I don't > >>>>> understand: > >>>>> -pbc atom -center (a group from index file) > >>>>> > >>>>> Thanks again for any other ideas... > >>>> I've only been loosely following this thread, but I've never had a > >>>> problem where trjconv didn't center as I wanted. Have you verified > that > >>>> the index group is correct, and you're making the proper selection? > What > >>>> does gmx traj report as the center-of-mass coordinates for those > groups > >>>> before and after trjconv tries to center them? > >>>> > >>>> -Justin > >>>> > >>>> -- > >>>> ================================================== > >>>> > >>>> Justin A. Lemkul, Ph.D. > >>>> Assistant Professor > >>>> Office: 301 Fralin Hall > >>>> Lab: 303 Engel Hall > >>>> > >>>> Virginia Tech Department of Biochemistry > >>>> 340 West Campus Dr. > >>>> Blacksburg, VA 24061 > >>>> > >>>> jalem...@vt.edu | (540) 231-3129 > >>>> http://www.thelemkullab.com > >>>> > >>>> ================================================== > >>>> > >>>> -- > >>>> Gromacs Users mailing list > >>>> > >>>> * Please search the archive at > >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>>> posting! > >>>> > >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>> > >>>> * For (un)subscribe requests visit > >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >>>> send a mail to gmx-users-requ...@gromacs.org. > >>>> > >> -- > >> ================================================== > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Office: 301 Fralin Hall > >> Lab: 303 Engel Hall > >> > >> Virginia Tech Department of Biochemistry > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalem...@vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> ================================================== > >> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Mala L. Radhakrishnan Whitehead Associate Professor of Critical Thought Associate Professor of Chemistry Wellesley College 106 Central Street Wellesley, MA 02481 (781)283-2981 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
