[gmx-users] How to use g_spatial?

[navnidhi rajput]

Hi,


I want to compute the spatial distribution function of solvents and around
cation. My system consists of 38 cations, 76 anions and 1266 solvent
molecules. Total 8774 atoms. I produced a trajectory from NVT simulation of
10ns. I used the following steps



Step1: gmx_sp trjconv -s nvt.tpr -f nvt.xtc -o b.xtc -boxcenter tric -ur
compact -pbc none

I selected system (group 0) for this option



Step2: gmx_sp trjconv -s nvt.tpr -f b.xtc  -o c.xtc -fit rot+trans

I selected first solvent and then cation


Select group for least squares fit

Group     0 (         System) has  8774 elements

Group     1 (            Ion) has    38 elements

Group     2 (             ZN) has    38 elements

Group     3 (            TFM) has  1140 elements

Group     4 (            ACL) has  7596 elements

Group     5 (          Other) has  8736 elements

Group     6 (             ZN) has    38 elements

Group     7 (            TFM) has  1140 elements

Group     8 (            ACL) has  7596 elements

Select a group: 8

Selected 8: 'ACL'

Select group for output

Group     0 (         System) has  8774 elements

Group     1 (            Ion) has    38 elements

Group     2 (             ZN) has    38 elements

Group     3 (            TFM) has  1140 elements

Group     4 (            ACL) has  7596 elements

Group     5 (          Other) has  8736 elements

Group     6 (             ZN) has    38 elements

Group     7 (            TFM) has  1140 elements

Group     8 (            ACL) has  7596 elements

Select a group: 6

Selected 6: 'ZN'

Reading frame       0 time    0.000

Precision of b.xtc is 0.001 (nm)

Using output precision of 0.001 (nm)

Last frame        200 time 10000.000    ->  frame    200 time 10000.000





Step3: gmx_sp spatial -f b.xtc -s nvt.tpr -n index.made.ndx

I select solvent (ACL) and cation (ZN) from the index files



I visualized the output grid.cube in VMD (isosurface, range: 0-7.872, Vol:
Isovalue 1, step: 1, Draw: Points, size:1, show:box+isosurface), looks like
I am only seeing the box if I select show: isosurface I see nothing.
However, if I select VDWor CPK format I only see some spheres.



I would really appreciate if you can you please let me know what I am doing
wrong?



Thanks,

Nav Nidhi Rajput