1# Simple virus model.
2#
3
4units lj
5dimension 3
6boundary f f f
7
8atom_style angle
9pair_style lj/cut 4.0
10pair_modify shift yes
11bond_style harmonic
12angle_style harmonic
13
14neigh_modify binsize 5.0
15
16read_data init.data
17
18group NC    type 1
19group rest  type 2 3 4
20group CA    type 3
21
22
23timestep 0.0001
24variable R equal "ramp(v_R0,v_R1)"
25
26variable RF equal ${R1}
27variable Rw equal "v_RF - 0.5"
28
29print "**** R scales from ${R0} to ${R1} and wall is at ${Rw} ****"
30
31variable rr   atom "sqrt( x*x + y*y + z*z )"
32compute  ravg CA reduce ave v_rr
33
34region my_sphere sphere 0 0 0 v_Rw side out
35fix wall all wall/region my_sphere lj126 1.0 1.0 1.1225
36
37
38variable U equal pe
39variable epair equal epair
40fix U all ave/time 2000 1 2000 v_U v_R v_epair
41variable t equal time
42variable ravg equal c_ravg
43
44variable T equal 0.25
45
46variable pU equal f_U[1]
47variable pE equal f_U[3]
48
49fix out all print 2000 "$t    ${pU}    $R    ${ravg}    ${pE}" file thermo.${DATA}.dat screen no
50
51fix step1 rest nvt temp $T $T 1.0
52fix step2 NC   nvt/manifold/rattle 1e-4 10 sphere v_R temp $T $T 1.0
53
54special_bonds lj 0 0 0
55
56angle_coeff 1 250.0 180.0
57
58thermo_style custom time step pe v_pU ke etotal epair temp v_R
59thermo 10000
60
61
62
63compute pe         all pe/atom
64fix     pe_avg     all ave/atom 100 50 5000 c_pe
65
66
67dump traj_all   all  custom 5000 virus.dump id type x   y   z f_pe_avg
68
69run 2500000
70unfix out
71
72fix step1 rest nvt temp $T $T 1.0
73fix step2 NC   nvt/manifold/rattle 1e-4 10 sphere ${R1} temp $T $T 1.0
74
75run 1000000
76