[gmx-users] gmx mindist error

[João Henriques]

"Is gmx mindist reading the box vector lengths from the structure file
instead?" ---> That would make no sense, since NPT simulations have varying
box sizes. Silly question, sorry. Still, I would really appreciate if
anyone could help me solving this issue.

J

On Tue, Mar 27, 2018 at 3:59 PM, João Henriques <
joao.m.a.henriques at gmail.com> 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?
>
> Thank you for your attention,
> Best regards,
> J
>