[gmx-users] Regarding calculation of SDF

[Dilip.H.N]

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