Re: [gmx-users] hbond error
On 2/16/17 9:17 AM, Mark Abraham wrote: Hi, Great. To check that I understand you, do you think it should it read "Ordering is the reverse of that in -hbn index file?" While this has been a point of confusion in the past, I think we have to be careful with the wording here. The ordering of -hbn and -hbm *is* actually the same (the first element in -hbn is in fact the first matrix element in -hbm), but the user has to understand how to interpret the contents of an .xpm file. Its contents are printed as one sees it visually, so the first line of data is the top line of the matrix, but that's not the first element of the matrix. So if we're going to clarify the language, we should probably have a rather more verbose explanation of how to map the entries, in terms of the .xpm content itself. -Justin Mark On Thu, Feb 16, 2017 at 2:32 PM wrote: Hi, I just realized that the hbond tool works fine, but produces output in reverse order. The "bug" is in the manual that states: * -hbm: existence matrix for all hydrogen bonds over all frames, this also contains information on solvent insertion into hydrogen bonds. Ordering is identical to that in -hbn index file. Chiara Il 16/02/17 13:41, *Mark Abraham * ha scritto: Hi, I'm not sure whether I properly understand your description of the behaviour. But if you think you have a case where the tool doesn't do what its documentation says, please open an issue at https://redmine.gromacs.org and attach a tarball of files that will help us diagnose and fix it :-) Mark On Thu, 16 Feb 2017 13:01 Chiara Parravicini < chiara.parravic...@guest.unimi.it> wrote: Dear Gmx users, using GROMACS version 2016.1, I found the following error in the output of the gmx hbond routine: when computed from different groups, where one is a subset of the other one, hbonds from the same acceptor/donor pair do not match. I known that this error has been already widely discussed in previous gromacs versions. Is there any solution? Thanks Chiara -- Chiara Parravicini, PhD Laboratorio di Biochimica e Biofisica Computazionale Dipartimento di Scienze Farmacologiche e Biomolecolari Università degli Studi di Milano Via Balzaretti 9, 20133 Milano, Italy Tel: +39 02-503-18256/18355 Fax: +39 02-503-18284 -- 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. -- Chiara Parravicini, PhD Laboratorio di Biochimica e Biofisica Computazionale Dipartimento di Scienze Farmacologiche e Biomolecolari Università degli Studi di Milano Via Balzaretti 9, 20133 Milano, Italy Tel: +39 02-503-18256/18355 Fax: +39 02-503-18284 -- 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] hbond error
Hi, Great. To check that I understand you, do you think it should it read "Ordering is the reverse of that in -hbn index file?" Mark On Thu, Feb 16, 2017 at 2:32 PM wrote: > Hi, > > I just realized that the hbond tool works fine, but produces output in > reverse order. The "bug" is in the manual that states: > > * -hbm: existence matrix for all hydrogen bonds over all frames, this > also > contains information on solvent insertion into hydrogen bonds. > Ordering is > identical to that in -hbn index file. > > Chiara > > Il 16/02/17 13:41, *Mark Abraham * ha scritto: > > Hi, > > > > I'm not sure whether I properly understand your description of the > > behaviour. But if you think you have a case where the tool doesn't do > what > > its documentation says, please open an issue at > > https://redmine.gromacs.org > > and attach a tarball of files that will help us diagnose and fix it :-) > > > > Mark > > > > On Thu, 16 Feb 2017 13:01 Chiara Parravicini < > > chiara.parravic...@guest.unimi.it> wrote: > > > > > Dear Gmx users, > > > > > > using GROMACS version 2016.1, I found the following error in the > > output of > > > the gmx hbond routine: when computed from different groups, where > > one is a > > > subset of the other one, hbonds from the same acceptor/donor pair do > not > > > match. > > > > > > I known that this error has been already widely discussed in previous > > > gromacs versions. Is there any solution? > > > > > > Thanks > > > > > > Chiara > > > > > > > > > > > > -- > > > Chiara Parravicini, PhD > > > Laboratorio di Biochimica e Biofisica Computazionale > > > Dipartimento di Scienze Farmacologiche e Biomolecolari > > > Università degli Studi di Milano > > > Via Balzaretti 9, > > > 20133 Milano, Italy > > > Tel: +39 02-503-18256/18355 > > > Fax: +39 02-503-18284 > > > > > > > > > -- > > > 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. > -- > Chiara Parravicini, PhD > Laboratorio di Biochimica e Biofisica Computazionale > Dipartimento di Scienze Farmacologiche e Biomolecolari > Università degli Studi di Milano > Via Balzaretti 9, > 20133 Milano, Italy > Tel: +39 02-503-18256/18355 > Fax: +39 02-503-18284 > > > -- > 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] hbond error
Hi, I just realized that the hbond tool works fine, but produces output in reverse order. The "bug" is in the manual that states: * -hbm: existence matrix for all hydrogen bonds over all frames, this also contains information on solvent insertion into hydrogen bonds. Ordering is identical to that in -hbn index file. Chiara Il 16/02/17 13:41, *Mark Abraham * ha scritto: Hi, I'm not sure whether I properly understand your description of the behaviour. But if you think you have a case where the tool doesn't do what its documentation says, please open an issue at https://redmine.gromacs.org and attach a tarball of files that will help us diagnose and fix it :-) Mark On Thu, 16 Feb 2017 13:01 Chiara Parravicini < chiara.parravic...@guest.unimi.it> wrote: > Dear Gmx users, > > using GROMACS version 2016.1, I found the following error in the output of > the gmx hbond routine: when computed from different groups, where one is a > subset of the other one, hbonds from the same acceptor/donor pair do not > match. > > I known that this error has been already widely discussed in previous > gromacs versions. Is there any solution? > > Thanks > > Chiara > > > > -- > Chiara Parravicini, PhD > Laboratorio di Biochimica e Biofisica Computazionale > Dipartimento di Scienze Farmacologiche e Biomolecolari > Università degli Studi di Milano > Via Balzaretti 9, > 20133 Milano, Italy > Tel: +39 02-503-18256/18355 > Fax: +39 02-503-18284 > > > -- > 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. -- Chiara Parravicini, PhD Laboratorio di Biochimica e Biofisica Computazionale Dipartimento di Scienze Farmacologiche e Biomolecolari Università degli Studi di Milano Via Balzaretti 9, 20133 Milano, Italy Tel: +39 02-503-18256/18355 Fax: +39 02-503-18284 -- 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] hbond error
Hi, I'm not sure whether I properly understand your description of the behaviour. But if you think you have a case where the tool doesn't do what its documentation says, please open an issue at https://redmine.gromacs.org and attach a tarball of files that will help us diagnose and fix it :-) Mark On Thu, 16 Feb 2017 13:01 Chiara Parravicini < chiara.parravic...@guest.unimi.it> wrote: > Dear Gmx users, > > using GROMACS version 2016.1, I found the following error in the output of > the gmx hbond routine: when computed from different groups, where one is a > subset of the other one, hbonds from the same acceptor/donor pair do not > match. > > I known that this error has been already widely discussed in previous > gromacs versions. Is there any solution? > > Thanks > > Chiara > > > > -- > Chiara Parravicini, PhD > Laboratorio di Biochimica e Biofisica Computazionale > Dipartimento di Scienze Farmacologiche e Biomolecolari > Università degli Studi di Milano > Via Balzaretti 9, > 20133 Milano, Italy > Tel: +39 02-503-18256/18355 > Fax: +39 02-503-18284 > > > -- > 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.
[gmx-users] hbond error
Dear Gmx users, using GROMACS version 2016.1, I found the following error in the output of the gmx hbond routine: when computed from different groups, where one is a subset of the other one, hbonds from the same acceptor/donor pair do not match. I known that this error has been already widely discussed in previous gromacs versions. Is there any solution? Thanks Chiara -- Chiara Parravicini, PhD Laboratorio di Biochimica e Biofisica Computazionale Dipartimento di Scienze Farmacologiche e Biomolecolari Università degli Studi di Milano Via Balzaretti 9, 20133 Milano, Italy Tel: +39 02-503-18256/18355 Fax: +39 02-503-18284 -- 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.
