[gmx-users] gmx mindist error

Tue Mar 27 23:55:58 CEST 2018

Yes, I understand what you and Justin refer to. Until your first email I
completely forgot to consider that certain simulations require variations
to the normal 3D periodicity, and thus my ramble about the box vectors. It
makes perfect sense now.

Also, thank you suggesting the alternative using the PDB, really
appreciated. It can certainly make things easier in this particular case.

Best regards,
J

On Tue, Mar 27, 2018 at 9:48 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Looking at the code, if your PDB file had suitable CRYST1 fields then you
> would not have needed a .tpr. I improved the docs a bit at
> https://gerrit.gromacs.org/#/c/7729/
>
> Mark
>
> On Tue, Mar 27, 2018 at 8:58 PM Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > 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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