G_mindist algorithm

User discussions
1

GROMACS version: 2021.1
GROMACS modification: No

I’m using g_mindist -on to calculate the number of water oxygens that are within a certain distance from the atoms of a ligand. Is the value outputted in numcont.xvg the number of water oxygens within the specified distance as computed from the atomic surfaces or the atomic centers of the ligand atoms?

2

From the atomic centers. You may be able to use the -d option to calculate how many are in contact (with the contact distance specified by you).

3

Thank you