[gmx-users] gmx mindist error

Fri Mar 30 00:16:07 CEST 2018

 ACEMD is very simplistic in the types of boxes: it only works with cubbic
boxes.

João

On Tue, Mar 27, 2018 at 10:55 PM, João Henriques <
joao.m.a.henriques at gmail.com> wrote:

> 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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-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613