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.

Header

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

Beads

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
...