[gmx-users] Spatial Distribution Function

Pandya, Akash akash.pandya.15 at ucl.ac.uk
Thu Sep 5 12:46:32 CEST 2019

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,


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