GROMACS version: 2021.4
GROMACS modification: No
I tried to analyze hydrogen bond between water-water. I am still confusing how to make index file containing donor (DH) and acceptor (A). Here is the result of my trial:
Reading file nvep.tpr, VERSION 2021.4-Ubuntu-2021.4-2 (single precision)
Specify 2 groups to analyze:
Group 0 ( System) has 30050 elements
Group 1 ( Other) has 8 elements
Group 2 ( URE) has 8 elements
Group 3 ( Water) has 30042 elements
Group 4 ( SOL) has 30042 elements
Group 5 ( non-Water) has 8 elements
Group 6 ( Water_&OW) has 10014 elements
Select a group: 3
Selected 3: ‘Water’
Select a group: 6
Selected 6: 'Water&OW’
Checking for overlap in atoms between Water and Water&_OW
I used water as DH, is it wrong?