[gmx-users] gmx mindist error

[Mark Abraham]

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.henriques at 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 <jalemkul at 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
> >
> > jalemkul at 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-request at 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-request at gromacs.org.