Re: [gmx-users] Problem with gmx trjconv -box -1 -1 14
Hi Mark it works. trjconv -box -1 -1 14 now change only the z dimension and maintains the original xy value present in the xtc file. Thanks again Stefano 2014-09-03 14:31 GMT+02:00 Mark Abraham : > Right - fix looks good. No need to do anything, Stefano, unless you'd like > to grab the source code and try out the solution at > https://gerrit.gromacs.org/#/c/3988/ > > Mark > > > On Wed, Sep 3, 2014 at 2:07 PM, Justin Lemkul wrote: > > > > > > > On 9/3/14, 7:52 AM, Mark Abraham wrote: > > > >> Hi, > >> > >> That does indeed contradict the docs. Can you please file an issue at > >> http://redmine.gromacs.org and attach your inputs and command line, so > we > >> can reproduce it? > >> > >> > > I think this comes from the fact that the code uses clear_mat(fr.box) and > > then only ever reassigns fr.box[m][m] in the case of newbox[m] > 0. If > > it's -1, then the code does nothing to it, so it stays at zero. Should > be > > a simple fix. > > > > -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. > -- --- Dr Stefano Borocci Laboratorio di Chimica e Chimica Computazionale Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali (DIBAF) Università degli Studi della Tuscia Largo dell'Università, snc 01100 Viterbo Tel. +39-0761-357127 +39-0761-357193 Fax +39 0761-357179 e-mail: boro...@unitus.it --- -- 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] Problem with gmx trjconv -box -1 -1 14
Hi Mark many thanks for your quick solution. I add the new lines to the source code and I try again the change of box size. Thanks Stefano 2014-09-03 14:31 GMT+02:00 Mark Abraham : > Right - fix looks good. No need to do anything, Stefano, unless you'd like > to grab the source code and try out the solution at > https://gerrit.gromacs.org/#/c/3988/ > > Mark > > > On Wed, Sep 3, 2014 at 2:07 PM, Justin Lemkul wrote: > > > > > > > On 9/3/14, 7:52 AM, Mark Abraham wrote: > > > >> Hi, > >> > >> That does indeed contradict the docs. Can you please file an issue at > >> http://redmine.gromacs.org and attach your inputs and command line, so > we > >> can reproduce it? > >> > >> > > I think this comes from the fact that the code uses clear_mat(fr.box) and > > then only ever reassigns fr.box[m][m] in the case of newbox[m] > 0. If > > it's -1, then the code does nothing to it, so it stays at zero. Should > be > > a simple fix. > > > > -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. > -- --- Dr Stefano Borocci Laboratorio di Chimica e Chimica Computazionale Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali (DIBAF) Università degli Studi della Tuscia Largo dell'Università, snc 01100 Viterbo Tel. +39-0761-357127 +39-0761-357193 Fax +39 0761-357179 e-mail: boro...@unitus.it --- -- 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] Problem with gmx trjconv -box -1 -1 14
Right - fix looks good. No need to do anything, Stefano, unless you'd like to grab the source code and try out the solution at https://gerrit.gromacs.org/#/c/3988/ Mark On Wed, Sep 3, 2014 at 2:07 PM, Justin Lemkul wrote: > > > On 9/3/14, 7:52 AM, Mark Abraham wrote: > >> Hi, >> >> That does indeed contradict the docs. Can you please file an issue at >> http://redmine.gromacs.org and attach your inputs and command line, so we >> can reproduce it? >> >> > I think this comes from the fact that the code uses clear_mat(fr.box) and > then only ever reassigns fr.box[m][m] in the case of newbox[m] > 0. If > it's -1, then the code does nothing to it, so it stays at zero. Should be > a simple fix. > > -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] Problem with gmx trjconv -box -1 -1 14
Hi Justin, I agree with you. The selection -box in trjconv create a new box and change all the dimension; If the value is -1, the original value of dimension (from the xtc file) is not maintained but changed to zero. Thanks Stefano 2014-09-03 14:07 GMT+02:00 Justin Lemkul : > > > On 9/3/14, 7:52 AM, Mark Abraham wrote: > >> Hi, >> >> That does indeed contradict the docs. Can you please file an issue at >> http://redmine.gromacs.org and attach your inputs and command line, so we >> can reproduce it? >> >> > I think this comes from the fact that the code uses clear_mat(fr.box) and > then only ever reassigns fr.box[m][m] in the case of newbox[m] > 0. If > it's -1, then the code does nothing to it, so it stays at zero. Should be > a simple fix. > > -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. > -- --- Dr Stefano Borocci Laboratorio di Chimica e Chimica Computazionale Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali (DIBAF) Università degli Studi della Tuscia Largo dell'Università, snc 01100 Viterbo Tel. +39-0761-357127 +39-0761-357193 Fax +39 0761-357179 e-mail: boro...@unitus.it --- -- 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] Problem with gmx trjconv -box -1 -1 14
On 9/3/14, 7:52 AM, Mark Abraham wrote: Hi, That does indeed contradict the docs. Can you please file an issue at http://redmine.gromacs.org and attach your inputs and command line, so we can reproduce it? I think this comes from the fact that the code uses clear_mat(fr.box) and then only ever reassigns fr.box[m][m] in the case of newbox[m] > 0. If it's -1, then the code does nothing to it, so it stays at zero. Should be a simple fix. -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.
Re: [gmx-users] Problem with gmx trjconv -box -1 -1 14
Hi, That does indeed contradict the docs. Can you please file an issue at http://redmine.gromacs.org and attach your inputs and command line, so we can reproduce it? Thanks, Mark On Wed, Sep 3, 2014 at 11:38 AM, Stefano Borocci wrote: > Hi all, > I am trying to use trjconv -box -1 -1 14 to modify the z dimention of the > box containing DMPC lipid bilayer and water. > I have used: > > trjconv -f dmpc.xtc -pbc mol -center -o dmpc_mol_cent.xtc -s dmpc.tpr > trjconv -f dmpc_mol_cent.xtc -o dmpc_newbox.xtc -box -1 -1 14 > > Both the modified version of trjconv (as reported in > http://redmine.gromacs.org/issues/871) and the gmx trjconv of GROMACS 5.0 > don't work. The -1 option in -box, for the x and y dimension, don't > preserve the original box size but changes these as 0: I obtain a box with > dimension 0 0 14. > > Thanks in advance > > > > Stefano > > -- > --- > Dr Stefano Borocci > Laboratorio di Chimica e Chimica Computazionale > Dipartimento per la Innovazione nei Sistemi Biologici, > Agroalimentari e Forestali (DIBAF) > Università degli Studi della Tuscia > Largo dell'Università, snc 01100 Viterbo > Tel. +39-0761-357127 > +39-0761-357193 > Fax +39 0761-357179 > e-mail: boro...@unitus.it > --- > -- > 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.
