[gmx-users] g_covar warnings
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? Thank you in advance, Best regards, João Henriques -- 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.
Re: [gmx-users] g_covar warnings
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.
Re: [gmx-users] g_covar warnings
On 3/27/14, 1:54 PM, João Henriques wrote: 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. Yes, if you have removed jumps and have intact structures throughout the trajectory, you're fine. The warning is only there for users who haven't thought ahead. -Justin /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. -- == 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.
Re: [gmx-users] g_covar warnings
Great, that's what I needed to know. Still, I totally agree with you. There are certain best practices, and using a .tpr is always the best choice. Thanks, João On Thu, Mar 27, 2014 at 7:02 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/27/14, 1:54 PM, João Henriques wrote: 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. Yes, if you have removed jumps and have intact structures throughout the trajectory, you're fine. The warning is only there for users who haven't thought ahead. -Justin /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. -- == 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.
