"Is gmx mindist reading the box vector lengths from the structure file instead?" ---> That would make no sense, since NPT simulations have varying box sizes. Silly question, sorry. Still, I would really appreciate if anyone could help me solving this issue.
J On Tue, Mar 27, 2018 at 3:59 PM, João Henriques < joao.m.a.henriq...@gmail.com> 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? > > Thank you for your attention, > Best regards, > J > -- 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.