[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 else is required?

Sorry if I am asking for much.


Regards,
Soumadwip Ghosh
Research Fellow
IITB
India