Hello Gromacs users,
I want to calculate hydrogen bonds over the trajectory, but only H-bonds
formed by a specific solute atom and any of the solvent molecules.
I typed the following command:
g_hbond -f md.trr -s md.tpr -n index.ndx -num hbnum -g hbond
and the index file specified contains the atom of interest (in group 3)
and all the water hydrogens (group 10):
-------
[ oxygen ]
556
[ solvent-O ]
6401 6404 6407 6410 6413 6416 6419 6422 6425 6428 6431 6434 6437 6440
6443 6446 6449 6452 6455 6458
(...) <<-- long list
-------
but what I get is this output:
-------
Specify 2 groups to analyze:
Group 0 ( phosphorus) has 1 elements
Group 1 ( carbon) has 1 elements
Group 2 ( nitrogen) has 1 elements
Group 3 ( oxygen) has 1 elements
Group 4 ( water) has 3 elements
Group 5 ( N-O) has 2 elements
Group 6 ( nitrogens) has 128 elements
Group 7 ( P8-C13) has 2 elements
Group 8 ( P8-C13-all) has 256 elements
Group 9 ( lipid1) has 50 elements
Group 10 ( solvent-O) has 3655 elements
Select a group: 3
Selected 3: 'oxygen'
Select a group: 10
Selected 10: 'solvent-O'
Checking for overlap in atoms between oxygen and solvent-O
Calculating hydrogen bonds between oxygen (1 atoms) and solvent-O (3655
atoms)
Found 0 donors and 3655 acceptors
No Donors found
Program g_hbond, VERSION 3.3.3
Source code file: gmx_hbond.c, line: 1911
Fatal error:
Nothing to be done
-------
Thank you for any hints
Grzegorz
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