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Dear GMX User.
I want to use gmx spatial to compute spatial distribution function of water
around solute (Protein).
After I typed the command: gmx spatial -s topol.tpr -f traj.trr -bin 0.05 -n
There are two options followed. I am very confused about those two options.
Is the first one for water and the second one for protein?
Or the first one for protein and the second one for protein?
Thanks!
Command line:
gmx spatial -s topol.tpr -f traj.trr -bin 0.05 -n
Reading file topol.tpr, VERSION 2019.6 (single precision)
Reading file topol.tpr, VERSION 2019.6 (single precision)
Select group to generate SDF:
Group 0 ( System) has 51203 elements
Group 1 ( Other) has 14 elements
Group 2 ( Protein) has 14 elements
Group 3 ( Water) has 51189 elements
Group 4 ( SOL) has 51189 elements
Group 5 ( non-Water) has 14 elements
Select a group: 3
Selected 3: ‘Water’
Select group to output coords (e.g. solute):
Group 0 ( System) has 51203 elements
Group 1 ( Other) has 14 elements
Group 2 ( Protein) has 14 elements
Group 3 ( Water) has 51189 elements
Group 4 ( SOL) has 51189 elements
Group 5 ( non-Water) has 14 elements
Select a group: 2
Selected 2: ‘Protein’
trr version: GMX_trn_file (single precision)
Tom