Re: [gmx-users] Double counting of h-bonds g_hbond:issue
Thanks Justin. It was the merging of the hbonds data that led to show the repetition of the list. If we do nomerge everything is reasonable. On Wed, Feb 18, 2015 at 7:41 AM, Justin Lemkul jalem...@vt.edu wrote: On 2/17/15 5:14 PM, Udaya Dahal wrote: Thanks Justin for prompt reply. Actually I calculated for the h_bonds with same criteria for (angle 30 and distance(D-A) 0.35nm) from VMD, and the number is lot less for both Polymer water and water water. I have 193 water molecules and the H-bond from VMD with same criteria gives me 232 H-bonds while GROMACS provides 340. The value GROMACS provides is better in the sense that it matches more closely to the experimental value but I kind of unsure since the visualization (in VMD ) also showed very few bonds. It shows like only 5 bonds from vmd calculation(and visualization) in previously mentioned Polymer water h-bonds. Probably VMD's plugin and g_hbond are doing something different. Note the VMD documentation seems to indicate the angle criteria is defined differently (D-H-A angle whereas g_hbond uses H-D-A, yet they use a similar value as a cutoff). Define a very small test system, something that you can literally look at and know the answer for sure, and see if the two programs agree. -Justin On Tue, Feb 17, 2015 at 7:58 AM, Justin Lemkul jalem...@vt.edu wrote: On 2/16/15 7:39 PM, Udaya Dahal wrote: Hi All, When I used the g_hbond the hydrogen bonding i was getting was quite good but when I checked the index file i find double counting of the bonds. So far, it seems to me that g_hbond is giving higher than the real hydrogen bonds present in the system. For eg. in the following OW-HW-oxygen, we see there are two bonds between 109(OW) and 110(HW) for two different polymer oxygens. Can anyone explain this issue? 76 77 12 100101 47 109110 40---1 (same hydrogen with two different oxygens) 109110 54---2(same hydrogen with two different oxygens) So does a visual inspection of this particular frame confirm that there shouldn't actually be hydrogen bonds with these atoms? This isn't double-counting, it's just a bit unusual, but is possible within the context of whatever criteria you have set for defining a hydrogen bond. -Justin 211212 54 211212 68 337338 68 343344 5 343344 19 403404 61 487488 5 511512 26 511512 40 538539 33 592593 12 592593 26 Hbnum.xvg shows hydrogen bonds pairs within 0.35 16 8 Regards, Udaya -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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 629 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] Double counting of h-bonds g_hbond:issue
On 2/17/15 5:14 PM, Udaya Dahal wrote: Thanks Justin for prompt reply. Actually I calculated for the h_bonds with same criteria for (angle 30 and distance(D-A) 0.35nm) from VMD, and the number is lot less for both Polymer water and water water. I have 193 water molecules and the H-bond from VMD with same criteria gives me 232 H-bonds while GROMACS provides 340. The value GROMACS provides is better in the sense that it matches more closely to the experimental value but I kind of unsure since the visualization (in VMD ) also showed very few bonds. It shows like only 5 bonds from vmd calculation(and visualization) in previously mentioned Polymer water h-bonds. Probably VMD's plugin and g_hbond are doing something different. Note the VMD documentation seems to indicate the angle criteria is defined differently (D-H-A angle whereas g_hbond uses H-D-A, yet they use a similar value as a cutoff). Define a very small test system, something that you can literally look at and know the answer for sure, and see if the two programs agree. -Justin On Tue, Feb 17, 2015 at 7:58 AM, Justin Lemkul jalem...@vt.edu wrote: On 2/16/15 7:39 PM, Udaya Dahal wrote: Hi All, When I used the g_hbond the hydrogen bonding i was getting was quite good but when I checked the index file i find double counting of the bonds. So far, it seems to me that g_hbond is giving higher than the real hydrogen bonds present in the system. For eg. in the following OW-HW-oxygen, we see there are two bonds between 109(OW) and 110(HW) for two different polymer oxygens. Can anyone explain this issue? 76 77 12 100101 47 109110 40---1 (same hydrogen with two different oxygens) 109110 54---2(same hydrogen with two different oxygens) So does a visual inspection of this particular frame confirm that there shouldn't actually be hydrogen bonds with these atoms? This isn't double-counting, it's just a bit unusual, but is possible within the context of whatever criteria you have set for defining a hydrogen bond. -Justin 211212 54 211212 68 337338 68 343344 5 343344 19 403404 61 487488 5 511512 26 511512 40 538539 33 592593 12 592593 26 Hbnum.xvg shows hydrogen bonds pairs within 0.35 16 8 Regards, Udaya -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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 629 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] Double counting of h-bonds g_hbond:issue
On 2/16/15 7:39 PM, Udaya Dahal wrote: Hi All, When I used the g_hbond the hydrogen bonding i was getting was quite good but when I checked the index file i find double counting of the bonds. So far, it seems to me that g_hbond is giving higher than the real hydrogen bonds present in the system. For eg. in the following OW-HW-oxygen, we see there are two bonds between 109(OW) and 110(HW) for two different polymer oxygens. Can anyone explain this issue? 76 77 12 100101 47 109110 40---1 (same hydrogen with two different oxygens) 109110 54---2(same hydrogen with two different oxygens) So does a visual inspection of this particular frame confirm that there shouldn't actually be hydrogen bonds with these atoms? This isn't double-counting, it's just a bit unusual, but is possible within the context of whatever criteria you have set for defining a hydrogen bond. -Justin 211212 54 211212 68 337338 68 343344 5 343344 19 403404 61 487488 5 511512 26 511512 40 538539 33 592593 12 592593 26 Hbnum.xvg shows hydrogen bonds pairs within 0.35 16 8 Regards, Udaya -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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.
[gmx-users] Double counting of h-bonds g_hbond:issue
Hi All, When I used the g_hbond the hydrogen bonding i was getting was quite good but when I checked the index file i find double counting of the bonds. So far, it seems to me that g_hbond is giving higher than the real hydrogen bonds present in the system. For eg. in the following OW-HW-oxygen, we see there are two bonds between 109(OW) and 110(HW) for two different polymer oxygens. Can anyone explain this issue? 76 77 12 100101 47 109110 40---1 (same hydrogen with two different oxygens) 109110 54---2(same hydrogen with two different oxygens) 211212 54 211212 68 337338 68 343344 5 343344 19 403404 61 487488 5 511512 26 511512 40 538539 33 592593 12 592593 26 Hbnum.xvg shows hydrogen bonds pairs within 0.35 16 8 Regards, Udaya -- 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.
