[gmx-users] gmx spatial

[Valerio Ferrario]

Dear Users,

I am trying to use the gmx spatial tool in order to understand how a solute
interact with the protein. I performed the calculation following all the
instructions (including the 2 trjconv steps). The trajectory obtained looks
fine, and I calculated the sdf with the following command:

gmx_mpi spatial -f CALBtrjvonv2.xtc -s CALBMpr-1.tpr -n X.ndx

and selecting the protein and an atom of my solute molecules (in the index)

but when I open the grid.cube file with vmd and I visualize it as
isosurface I have the density function even within the protein core... I
thought that the density should be just around the protein (in this case).
Moreover I have just positive values for the isosurface, is that normal? Am
I doing something wrong?

Thanks a lot,
Valerio Ferrario