I see, I didn't consider that. I was strictly thinking about the geometry of the box.
Anyway, with some tricks I managed to build a tpr and am now able to calculate the mindist to the periodic image. Thanks! J On 18:19, Tue, Mar 27, 2018 Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > The box sizes say nothing about whether the boundary is fully or partially > periodic, or screw, or not. > > Mark > > On Tue, Mar 27, 2018, 16:13 João Henriques <joao.m.a.henriq...@gmail.com> > wrote: > > > Thanks Justin, I was really trying to avoid making a tpr file, because my > > ACEMD uses the Amber format. I sort of hoped gmx mindist could figure it > > out from the box components present in the xtc file. In principle, > couldn't > > it be done by using that info alone? Just curious. > > > > J > > > > On Tue, Mar 27, 2018 at 4:04 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > > > > > On 3/27/18 9:59 AM, João Henriques wrote: > > > > > >> Dear users and developers, > > >> > > >> I am trying to use gmx mindist to calculate the minimum distance > between > > >> periodic images but I get the following error: > > >> > > >> Fatal error: > > >> pbc = no is not supported by g_mindist > > >> > > >> This is the command I am running: > > >> > > >> gmx_mpi mindist -f output.xtc -s structure.pdb -od -pi -pbc > > >> > > >> Now, I have to admit that the .xtc file I'm using is generated by > ACEMD > > >> and > > >> not mdrun, but I used gmx dump to check it and everything looks sane. > > The > > >> cuboid box sizes are clearly specified and I don't understand what the > > >> problem is... > > >> > > >> box (3x3): > > >> box[ 0]={ 8.16756e+00, 0.00000e+00, 0.00000e+00} > > >> box[ 1]={ 0.00000e+00, 8.25175e+00, 0.00000e+00} > > >> box[ 2]={ 0.00000e+00, 0.00000e+00, 9.73586e+00} > > >> > > >> Is gmx mindist reading the box vector lengths from the structure file > > >> instead? > > >> > > > > > > When you don't provide a .tpr file, the program does not know what type > > of > > > periodicity the simulation used, so it cannot do the requested > > calculation > > > because the shifts cannot be calculated. > > > > > > -Justin > > > > > > -- > > > ================================================== > > > > > > Justin A. Lemkul, Ph.D. > > > Assistant Professor > > > Virginia Tech Department of Biochemistry > > > > > > 303 Engel Hall > > > 340 West Campus Dr. > > > Blacksburg, VA 24061 > > > > > > jalem...@vt.edu | (540) 231-3129 > > > http://www.thelemkullab.com > > > > > > ================================================== > > > > > > -- > > > 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. > -- > 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.