[gmx-users] gmx mindist error

[Mark Abraham]

Hi,

I have no idea how ACEMD works, but one can certainly imagine an MD package
that hard codes the assumption of a cubic box with normal 3D periodicity.
But there's nothing intrinsic to the file format that implies any
periodicity to a box. That's either a convention, or given by other
information from the user.

Mark

On Tue, Mar 27, 2018, 18:26 João Henriques <joao.m.a.henriques at gmail.com>
wrote:

> 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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