[gmx-users] g_spatial Problem

[Rubaiyet Abedin]

Dear Sir,

Hope you are doing good. I am working with a system that contains ionic
liquid and refrigerant. To avoid complication let’s say my system contains
the following:

Cation (1)

Anion (2)

Type A (3)

Type B (4)



And the system (0). I want to get the spatial distribution function of type
A around Anion. So the central molecule will be the anion. I used the
following commands:



*1.      **make_ndx -f bath_298K.part0001.gro -o bath_298K_index.ndx*



*2.      **trjconv -s bath_298K.tpr -f bath_298K.part0001.xtc -o
bath_298K_b.xtc -center  -ur compact -pbc none  -n bath_298K_index.ndx*



I selected Anion (2) for centering and system (0) for output



*3.      **trjconv -s bath_298K.tpr -f bath_298K_b.xtc -o bath_298K_c.xtc
-fit rot+trans*



I selected Anion (2) for fitting and system (0) for output



*4.      **g_spatial -s bath_298K.tpr -f bath_298K_c.xtc -n
bath_298K_index.ndx -nab 100*



I selected Anion (2) to generate SDF and type A (3) to output coordinates



*5.      **g_spatial -s bath_298K.tpr -f bath_298K_c.xtc -n
bath_298K_index.ndx -nab 100*



I selected Anion (2) to generate SDF and Anion (2) to output coordinates



I got two grid.cube file and load them into vmd. For the grid.cube (from
step 4) I chose the isosurface value 0.01 and viewed the other cube file as
a single molecule. I have several question:



1.      Do you think I am following the right procedure specially I am
confused and step 4 and 5. After loading both of the grid.cube file I got
something like this the attached.

 For some cases I even got rectangular box. Should it be a sphere?

2.      I am choosing a random Anion (2). Every time I choose a different
anion, I see different cloud shape. I am confused if I am doing something
wrong or I have to choose the central molecule following any specific
technique.


Please help me out with this. Thanks a lot.



Rubaiyet