[gmx-users] gmx mindist error

[Mark Abraham]

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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