[gmx-users] Regarding calculation of SDF

[Mark Abraham]

Hi,

I can't tell whether you have a corrupted file, GROMACS has buggy code, or
the analysis procedure is wrong.

Mark

On Mon, May 28, 2018 at 4:18 AM Dilip.H.N <cy16f01.dilip at nitk.edu.in> wrote:

> Hi,
> I want to calculate the Spatial Distribution Function of say N-terminal
> nitrogen atom and all the oxygen atoms of the water molecules.
> So, i have created the index file in which i have the nitrogen atom and all
> the oxygen atoms of water molecules. And here are my commands that i gave
> inorder to calculate SDF:
> gmx trjconv -s nptmd.tpr -f nptmd.xtc -n ndx_NOw.ndx -o abc.tng -ur compact
> -pbc whole
> gmx trjconv -s nptmd.tpr -f abc.tng -n ndx_NOw.ndx -o def.tng -fit
> rot+trans
> gmx spatial -s nptmd.tpr -n ndx_NOw.ndx -f def.tng -nab 10
>
> I get the following:
> Reading file nptmd.tpr, VERSION 2016.2 (single precision)
> Select group to generate SDF:
> Group     0 (             N) has     1 elements
> Group     1 (             OW) has   511 elements
> Select a group: 0
> Selected 0: 'N'
> Select group to output coords (e.g. solute):
> Group     0 (             N) has     1 elements
> Group     1 (             OW) has   511 elements
> Select a group: 1
> Selected 1: 'OW'
> TNG library: Cannot uncompress data block.
> /home/dilip/Downloads/gromacs-2016.2/src/external/tng_io/src/lib/tng_io.c:
> 5298
> TNG library: Cannot uncompress data block.
> /home/dilip/Downloads/gromacs-2016.2/src/external/tng_io/src/lib/tng_io.c:
> 5298
> Last frame      60000 time 30000.000
> Back Off! I just backed up grid.cube to ./#grid.cube.1#
> Counts per frame in all 27 cubes divided by 3.703704e-02
> Normalized data: average 1.000000e+00, min 0.000000e+00, max 2.700000e+01
>
>
> and if i view the grid.cube file in vmd, i am unable to get a proper SDF/it
> is wired when i give an isovalues and change its values...
>
> How can i solve this..??
> Any suggestions are highly appreciated.
>
> Thank you.
>
> ---
> With Best Regards,
>
> Dilip.H.N
> PhD Student.
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> 05/28/18,
> 7:47:09 AM
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