[gmx-users] Using g_spatial

[soumadwip ghosh]

Hi,
    I am interested in calculating the SDF and visualize the solvation
structure of Fullerene in the first solvation shell in presence and in
absence of water soluble binders. I have never used g_spatial. Form
the instruction I came to know about stuffs like the grid.cube file to
be uploaded in VMD and visualize in isosurface mode. However, I have
some questions-


1. While executing trjconv twice should I select the whole system (0)
as output group of trjconv?
2. If I have a hybrid (fullerene+ binder) and SOL in my custom index
group which are to be chosen as groups 1 and 2 respectively? Is it
like selecting SOL as 1 and selecting hybrid as 2 as 2 asks for solute
molecules?


3. In order to visualize a pretty figure ( those reported in papers)
is it sufficient to load grid.cube in the VMD and see it in isosurface
mode or something additional is also required?


Sorry if I am asking for much.




Regards,
Soumadwip Ghosh
Research Fellow
IITB
India