[gmx-users] gmx mindist error

[Justin Lemkul]

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

==================================================