Project ID: plumID:21.030
Source: nspe/cn.dat

#! vim:ft=plumed


# coordination 
r1: COM ATOMS=13,22 #res 1 and 10 agg in trial 1
r2: COM ATOMS=41,50
r3: COM ATOMS=64,73
r4: COM ATOMS=87,96
r5: COM ATOMS=110,119
r6: COM ATOMS=133,142 #res 6 and 9 should be coordinated in a helix
r7: COM ATOMS=156,165
r8: COM ATOMS=179,188
r9: COM ATOMS=202,211 #CG-CH 
r10: COM ATOMS=225,234
r11: COM ATOMS=248,257
r12: COM ATOMS=270,279

#distances (12*11)/2 = 66 pairs?
d1-2: DISTANCE ATOMS=r1,r2
d1-3: DISTANCE ATOMS=r1,r3
d1-4: DISTANCE ATOMS=r1,r4
d1-5: DISTANCE ATOMS=r1,r5
d1-6: DISTANCE ATOMS=r1,r6
d1-7: DISTANCE ATOMS=r1,r7
d1-8: DISTANCE ATOMS=r1,r8
d1-9: DISTANCE ATOMS=r1,r9
d1-10: DISTANCE ATOMS=r1,r10
d1-11: DISTANCE ATOMS=r1,r11
d1-12: DISTANCE ATOMS=r1,r12
d2-3: DISTANCE ATOMS=r2,r3
d2-4: DISTANCE ATOMS=r2,r4
d2-5: DISTANCE ATOMS=r2,r5
d2-6: DISTANCE ATOMS=r2,r6
d2-7: DISTANCE ATOMS=r2,r7
d2-8: DISTANCE ATOMS=r2,r8
d2-9: DISTANCE ATOMS=r2,r9
d2-10: DISTANCE ATOMS=r2,r10
d2-11: DISTANCE ATOMS=r2,r11
d2-12: DISTANCE ATOMS=r2,r12
d3-4: DISTANCE ATOMS=r3,r4
d3-5: DISTANCE ATOMS=r3,r5
d3-6: DISTANCE ATOMS=r3,r6
d3-7: DISTANCE ATOMS=r3,r7
d3-8: DISTANCE ATOMS=r3,r8
d3-9: DISTANCE ATOMS=r3,r9
d3-10: DISTANCE ATOMS=r3,r10
d3-11: DISTANCE ATOMS=r3,r11
d3-12: DISTANCE ATOMS=r3,r12
d4-5: DISTANCE ATOMS=r4,r5
d4-6: DISTANCE ATOMS=r4,r6
d4-7: DISTANCE ATOMS=r4,r7
d4-8: DISTANCE ATOMS=r4,r8
d4-9: DISTANCE ATOMS=r4,r9
d4-10: DISTANCE ATOMS=r4,r10
d4-11: DISTANCE ATOMS=r4,r11
d4-12: DISTANCE ATOMS=r4,r12
d5-6: DISTANCE ATOMS=r5,r6
d5-7: DISTANCE ATOMS=r5,r7
d5-8: DISTANCE ATOMS=r5,r8
d5-9: DISTANCE ATOMS=r5,r9
d5-10: DISTANCE ATOMS=r5,r10
d5-11: DISTANCE ATOMS=r5,r11
d5-12: DISTANCE ATOMS=r5,r12
d6-7: DISTANCE ATOMS=r6,r7
d6-8: DISTANCE ATOMS=r6,r8
d6-9: DISTANCE ATOMS=r6,r9
d6-10: DISTANCE ATOMS=r6,r10
d6-11: DISTANCE ATOMS=r6,r11
d6-12: DISTANCE ATOMS=r6,r12
d7-8: DISTANCE ATOMS=r7,r8
d7-9: DISTANCE ATOMS=r7,r9
d7-10: DISTANCE ATOMS=r7,r10
d7-11: DISTANCE ATOMS=r7,r11
d7-12: DISTANCE ATOMS=r7,r12
d8-9: DISTANCE ATOMS=r8,r9
d8-10: DISTANCE ATOMS=r8,r10
d8-11: DISTANCE ATOMS=r8,r11
d8-12: DISTANCE ATOMS=r8,r12
d9-10: DISTANCE ATOMS=r9,r10
d9-11: DISTANCE ATOMS=r9,r11
d9-12: DISTANCE ATOMS=r9,r12
d10-11: DISTANCE ATOMS=r10,r11
d10-12: DISTANCE ATOMS=r10,r12
d11-12: DISTANCE ATOMS=r11,r12

# coordination
c: COORDINATION GROUPA=r1,r1,r1,r1,r1,r1,r1,r1,r1,r1,r1,r2,r2,r2,r2,r2,r2,r2,r2,r2,r2,r3,r3,r3,r3,r3,r3,r3,r3,r3,r4,r4,r4,r4,r4,r4,r4,r4,r5,r5,r5,r5,r5,r5,r5,r6,r6,r6,r6,r6,r6,r7,r7,r7,r7,r7,r8,r8,r8,r8,r9,r9,r9,r10,r10,r11  GROUPB=r2,r3,r4,r5,r6,r7,r8,r9,r10,r11,r12,r3,r4,r5,r6,r7,r8,r9,r10,r11,r12,r4,r5,r6,r7,r8,r9,r10,r11,r12,r5,r6,r7,r8,r9,r10,r11,r12,r6,r7,r8,r9,r10,r11,r12,r7,r8,r9,r10,r11,r12,r8,r9,r10,r11,r12,r9,r10,r11,r12,r10,r11,r12,r11,r12,r12 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10 PAIR

# each ring coord
c1: COORDINATION GROUPA=r1 GROUPB=r2 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10 
c2: COORDINATION GROUPA=r1 GROUPB=r3 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10 
c3: COORDINATION GROUPA=r1 GROUPB=r4 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10 
c4: COORDINATION GROUPA=r1 GROUPB=r5 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10 
c5: COORDINATION GROUPA=r1 GROUPB=r6 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10 
c6: COORDINATION GROUPA=r1 GROUPB=r7 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10 
c7: COORDINATION GROUPA=r1 GROUPB=r8 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10 
c8: COORDINATION GROUPA=r1 GROUPB=r9 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10 
c9: COORDINATION GROUPA=r1 GROUPB=r10 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10 
c10: COORDINATION GROUPA=r1 GROUPB=r11 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10 
c11: COORDINATION GROUPA=r1 GROUPB=r12 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10 
c12: COORDINATION GROUPA=r2 GROUPB=r3 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c13: COORDINATION GROUPA=r2 GROUPB=r4 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10 
c14: COORDINATION GROUPA=r2 GROUPB=r5 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10 
c15: COORDINATION GROUPA=r2 GROUPB=r6 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10 
c16: COORDINATION GROUPA=r2 GROUPB=r7 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10 
c17: COORDINATION GROUPA=r2 GROUPB=r8 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10 
c18: COORDINATION GROUPA=r2 GROUPB=r9 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10 
c19: COORDINATION GROUPA=r2 GROUPB=r10 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10 
c20: COORDINATION GROUPA=r2 GROUPB=r11 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10 
c21: COORDINATION GROUPA=r2 GROUPB=r12 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c22: COORDINATION GROUPA=r3 GROUPB=r4 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c23: COORDINATION GROUPA=r3 GROUPB=r5 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c24: COORDINATION GROUPA=r3 GROUPB=r6 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c25: COORDINATION GROUPA=r3 GROUPB=r7 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c26: COORDINATION GROUPA=r3 GROUPB=r8 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c27: COORDINATION GROUPA=r3 GROUPB=r9 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c28: COORDINATION GROUPA=r3 GROUPB=r10 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c29: COORDINATION GROUPA=r3 GROUPB=r11 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c30: COORDINATION GROUPA=r3 GROUPB=r12 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c31: COORDINATION GROUPA=r4 GROUPB=r5 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c32: COORDINATION GROUPA=r4 GROUPB=r6 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c33: COORDINATION GROUPA=r4 GROUPB=r7 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c34: COORDINATION GROUPA=r4 GROUPB=r8 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c35: COORDINATION GROUPA=r4 GROUPB=r9 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c36: COORDINATION GROUPA=r4 GROUPB=r10 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c37: COORDINATION GROUPA=r4 GROUPB=r11 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c38: COORDINATION GROUPA=r4 GROUPB=r12 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c39: COORDINATION GROUPA=r5 GROUPB=r6 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c40: COORDINATION GROUPA=r5 GROUPB=r7 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c41: COORDINATION GROUPA=r5 GROUPB=r8 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c42: COORDINATION GROUPA=r5 GROUPB=r9 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c43: COORDINATION GROUPA=r5 GROUPB=r10 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c44: COORDINATION GROUPA=r5 GROUPB=r11 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c45: COORDINATION GROUPA=r5 GROUPB=r12 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c46: COORDINATION GROUPA=r6 GROUPB=r7 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c47: COORDINATION GROUPA=r6 GROUPB=r8 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c48: COORDINATION GROUPA=r6 GROUPB=r9 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c49: COORDINATION GROUPA=r6 GROUPB=r10 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c50: COORDINATION GROUPA=r6 GROUPB=r11 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c51: COORDINATION GROUPA=r6 GROUPB=r12 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c52: COORDINATION GROUPA=r7 GROUPB=r8 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c53: COORDINATION GROUPA=r7 GROUPB=r9 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c54: COORDINATION GROUPA=r7 GROUPB=r10 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c55: COORDINATION GROUPA=r7 GROUPB=r11 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c56: COORDINATION GROUPA=r7 GROUPB=r12 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c57: COORDINATION GROUPA=r8 GROUPB=r9 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c58: COORDINATION GROUPA=r8 GROUPB=r10 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c59: COORDINATION GROUPA=r8 GROUPB=r11 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c60: COORDINATION GROUPA=r8 GROUPB=r12 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c61: COORDINATION GROUPA=r9 GROUPB=r10 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c62: COORDINATION GROUPA=r9 GROUPB=r11 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c63: COORDINATION GROUPA=r9 GROUPB=r12 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c64: COORDINATION GROUPA=r10 GROUPB=r11 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c65: COORDINATION GROUPA=r10 GROUPB=r12 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10
c66: COORDINATION GROUPA=r11 GROUPB=r12 R_0=0.5 NN=8 MM=12  NLIST NL_CUTOFF=0.75 NL_STRIDE=10