hbond_analysis is a  member of SPANA and the parallelized version of hb_analysis. This tool is parallelized with hybrid MPI/OpenMP.  Like hb_analysis, we need the three geometrical parameters for the detection of H-bond:  hb_distance (d), HDA_angle (α), and DHA_angle (β). In the default, d = 3.4 Å, α = 30.0 deg. and β = 120.0 deg, and if you use your own definition, you can specify these value in [HBOND_OPTION].

Hbond_analysis tool is useful to examine H-bond patterns for a huge protein molecule or for crowding system. You can limit the range used for the analysis (for example, focus on H-bonds around ligand-binding site or in hydrophilic channel) by adequately using determine_box = MANUAL option.

Functions of this tool is same as hb_analysis except this analysis is done with space_decomposition. Thus, when you need a H-bond list written in hb_listfile, the hb_listfile is output per domain. When you specify hb_listfile name, you need () to return MPI process numbers. The parameter cutoff is important to determine the range to search H-bond partners of analysis_atom. The cutoff value should be larger than the hb_distance value.

Unlike hb_analysis, to wrap molecules into the PBC box, we need the use of the options recenter and wrap to correctly detect H-bonds formed between analysis_atom and target_atom.

[INPUT]
psffile = BPTI_ionize.psf
reffile = BPTI_ionize.pdb

[OUTPUT]
txtfile     = BPTI-wat_Hbond.txt
hblist_file = BPTI_wat_hbond_mpi().list

[TRAJECTORY]
trjfile1      = run.dcd
md_step1      = 10
mdout_period1 = 1
ana_period1   = 1

trj_format    = DCD
trj_type      = COOR+BOX

[ENSEMBLE]
ensemble      = NPT

[BOUNDARY]
type          = PBC
domain_x      = 2
domain_y      = 2
domain_z      = 1
num_cells_x   = 10
num_cells_y   = 10
num_cells_z   = 10
box_size_x    = 50.0
box_size_y    = 50.0
box_size_z    = 50.0

[SELECTION]
group1        = sid:BPTI & resno:1-58
group2        = resname:TIP3
group3        = sid:BPTI & (resno:3 | resno:7-8 | resno:39-40 | resno:43)

[SPANA_OPTION]
wrap          = yes      # wrap molecules if wrap = yes 
buffer        = 5.0      # this distance should be larger than hb_distance.
box_size      = TRAJECTORY # (TRAJECTORY / MANUAL / MAX)

[HBOND_OPTION]
recenter      = 3 
output_type   = count_atom    # (count_atom / count_snap)
analysis_atom = 1
target_atom   = 2
solvent_list  = TIP3
# hb_distance   =   3.4   # upper limit of distance between Donor and Acceptor atoms, default value is 3.4 A
# dha_angle     =  30.0   # upper limit of H-bond D-H..A angle, default value is  30.0 deg.
# hda_angle     = 120.0   # lower limit of H-bond H-D..A angle, default value is 120.0 deg.

Updated: