Input File Generation
You can easily make your own input file for any virus capsomere! SOUFFLE reads an input file of the capsomere and propagates the simulation box with copies of that capsomere. Currently only a single type of capsomere is permitted, but adding multiple types is something we are working on adding.
Each subunit has three essential components:
- Bead
- Edges -- the bonds between the beads
- Faces -- A plane between 3 beads
We will briefly go over how to incorporate each of these elements into your input file.
The beginning of the files should have the following header information:
ks_vdwr = 1.122462048
mass = 1.05e-24
sigma = 1e-9
ks_vdwr is the value of sigma^(1/6), this is taken as a constant in the code. mass is the unit mass for the system in kg, usually taken as the mass for the smallest bead. sigma is the unit length for the system in m, usually taken as the diameter for the smallest bead
Input the coordinates, type, charge, diameter and mass in reduced units for each bead. Types should be different for beads that have differing diameters or LJ-attraction properties. Type 5 and 6 are reserved for beads with a diameter greater than 1. This is hard-coded currently and will be modified in the next code version.
# Number of Beads = 41
index x y z type charge diameter mass
0 2.244924096 7.77664518681526 0 3 0 1 1
1 1.683693072 6.80456453846336 0 1 0 1 1
2 2.80615512 6.80456453846336 0 2 0 1 1
...
Input the bead indexes the edges are between, edge length and edge type. Edge type refers to whether or not an edge is a bending edge. Bending edges are between two faces that have parallel normal angles and have type 1. Non-bending edges have type 0.
# Number of Edges = 119
index bead_1 bead_2 type length
0 0 1 0 1.122462048
1 0 2 0 1.122462048
2 1 2 1 1.122462048
...
Input the indexes of beads within a face, type (always 0) and normal. Counting beads clockwise has a normal of 1 and counterclockwise -1.
# Number of Triangles = 76
index bead_1 bead_2 bead_3 type normal
0 0 1 2 0 1
1 1 3 39 0 1
2 2 39 4 0 1
...
Input the attractive pairs of bead types, epsilon, and sigma_hc (hard core sigma). Sigma_hc is 1 unless the attractive pairs are between beads of differing sizes. If type A and B are attractive, you must list it twice, A-B and B-A as in the example below:
# Number of LJ Attractions = 4
index bead_type1 bead_type2 epsilon sigmahc
0 1 2 2 1
1 2 1 2 1
2 3 3 2 1
...