contact_analysis
contact_analysis calculates number of contact (atom pairs whose distance is smaller than the range) between the groups specified in the section [SELECTION]. Image atoms around the unit box are also included in the analysis if the boundary type is PBC.
(EX1) Multiple villins under the crowding condition
In this example, number of contacts between multiple (22) villins in crowding condition are calculated. The matrix of the contact numbers between the group_ij are output when mode=number is specified.
[INPUT]
psffile = villin_crowding.psf
reffile = villin_crowding.pdb
[OUTPUT]
txtfile = villin_number.out
[TRAJECTORY]
trjfile1 = prod.dcd
md_step1 = 10000
mdout_period1 = 500
ana_period1 = 500
repeat1 = 1
trj_format = DCD
trj_type = COOR+BOX
[BOUNDARY]
type = PBC
box_size_x = 142
box_size_y = 142
box_size_z = 142
domain_x = 2
domain_y = 2
domain_z = 2
num_cells_x = 14
num_cells_y = 14
num_cells_z = 14
[ENSEMBLE]
ensemble = NPT
[SELECTION]
group1 = ai: 1 - 596
group2 = ai: 597 - 1192
group3 = ai: 1193 - 1788
group4 = ai: 1789 - 2384
group5 = ai: 2385 - 2980
group6 = ai: 2981 - 3576
group7 = ai: 3577 - 4172
group8 = ai: 4173 - 4768
group9 = ai: 4769 - 5364
group10 = ai: 5365 - 5960
group11 = ai: 5961 - 6556
group12 = ai: 6557 - 7152
group13 = ai: 7153 - 7748
group14 = ai: 7749 - 8344
group15 = ai: 8345 - 8940
group16 = ai: 8941 - 9536
group17 = ai: 9537 - 10132
group18 = ai: 10133 - 10728
group19 = ai: 10729 - 11324
group20 = ai: 11325 - 11920
group21 = ai: 11921 - 12516
group22 = ai: 12517 - 13112
[SPANA_OPTION]
buffer = 10
wrap = yes
box_size = TRAJECTORY
[CONTACT_OPTION]
range = 10
mode = number
mode=mindist outputs atomic pairs which gives the minimum distance between group_ij.
[CONTACT_OPTION] mode = mindist