[gmx-users] Spatial Distribution Function

[Pandya, Akash]

Hi all,

I'm trying to generate a spatial distribution function for my ligands around my protein. I read in the manual I can bypass the gmx trjconv steps if I wanted to calculate the SDF for arbitrary Cartesian coordinates. The command I used is shown below:

gmx spatial -f protein_LIG.gro -s protein.tpr -n LIG.ndx -b 20000 -e 60000 -w yes -nab 10

I selected the LIG group for the SDF calculation and selected the protein and LIG group for the output coordinates. Is this correct? Any help would be much appreciated.


Best wishes,

Akash