[gmx-users] gmx mindist error

[João Henriques]

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.abraham at 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.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
> > >
> > > ==================================================
> > >
> > > --
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