Thanks Justin. That corroborates my "no .tpr, no party" suspicion. However, would it be possible to achieve a correct analysis if I were to use a whole .gro with a properly pre-processed .xtc (-ur -pbc)? Maybe I didn't explain myself properly, but that's what I want to know.
/J On Thu, Mar 27, 2014 at 6:32 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/27/14, 1:27 PM, João Henriques wrote: > >> Hello everyone, >> >> The documentation reads: >> >> """ >> All structures are fitted to the structure in the structure file. When >> this >> is not a run input file periodicity will not be taken into account. >> """ >> >> This is rather cryptic, what does it mean in practice? No tpr, no party? >> What if I use a properly centered and whole .gro file? >> >> When ran with a .gro as the structure input file, I get two warnings. One >> is related to the masses, which are non-existent in the .gro, but I don't >> need them anyway. The second warning is honestly confusing me even more. >> >> """ >> WARNING: If there are molecules in the input trajectory file >> that are broken across periodic boundaries, they >> cannot be made whole (or treated as whole) without >> you providing a run input file. >> """ >> >> The documentation points out to the structure input file and now it's the >> trajectory? What's going on? Do I also need to make each frame whole in >> the >> input .xtc? Can someone elaborate on this? >> >> > The documentation consistently refers to the run input file. A .tpr has > record of how periodicity is treated. Nothing else does. If you don't > tell g_covar (like most Gromacs tools) how periodicity is treated, you can > get garbage as a result. The trajectory may have "broken" molecules, > because mdrun doesn't care how they look - it has a run input file and thus > knowledge of periodicity. When running analysis like g_covar, if the > bonded connectivity of the molecule and the periodicity are unknown (again, > if you're not using a .tpr), then absolute displacements of coordinates are > used, thus your analysis might be totally hosed if the molecule "splits" - > that would be a rather dramatic structure change detected by g_covar. In > fact, so dramatic that it's false. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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.