[gmx-users] gmx mindist error

[João Henriques]

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
>
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