[gmx-users] Regarding calculation of SDF

[Dallas Warren]

What exactly is the issue?  It isn't clear what the problem is; the
fact it is having trouble with using the tng file format, or the
output in the cube file that is then loaded into vmd?
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 28 May 2018 at 12:17, 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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