[gmx-users] g_spatial index file

Paymon Pirzadeh ppirzade at ucalgary.ca
Thu Feb 16 05:03:44 CET 2012

I used g_select to choose the hydration shell molecules of my protein
from a trajectory of 15ns saved every 10ps (1500 frames). Now I want to
feed the generated index file into g_spatial to calculate the SDF of
solvent around my protein. However, when I feed this into the g_spatial,
it lists 1500 group and my protein. How can I tell the command to use
the 1500 groups to calculate the SDF?
Or can I specify a dynamic selection when I run the g_spatial? sth like
"resname SOL and within 1.0 of protein"?


More information about the gromacs.org_gmx-users mailing list