[gmx-users] gmx mindist error

Justin Lemkul jalemkul at vt.edu
Tue Mar 27 16:05:15 CEST 2018

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 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


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