cyclohexane-twist-boat.mbsf is added to the repository

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@406 a2be9bc6-48de-4e38-9406-05402d4bc13c

diff --git a/Scripts/mbsf/alicyclic/cyclohexane-twist-boat.mbsf b/Scripts/mbsf/alicyclic/cyclohexane-twist-boat.mbsf
new file mode 100644 (file)
index 0000000..6ca0666
--- /dev/null
+++ b/Scripts/mbsf/alicyclic/cyclohexane-twist-boat.mbsf
@@ -0,0 +1,206 @@
+!:atoms
+! idx seg_name res_seq res_name name type charge weight element atomic_number occupancy temp_factor int_charge
+0 MAIN 1 CHX C1 c3 0.02028 12.01070 C 6 1.000000 0.000000 0
+1 MAIN 1 CHX H11 hc -0.01014 1.00790 H 1 1.000000 0.000000 0
+2 MAIN 1 CHX H12 hc -0.01014 1.00790 H 1 1.000000 0.000000 0
+3 MAIN 1 CHX C2 c3 0.02028 12.01070 C 6 1.000000 0.000000 0
+4 MAIN 1 CHX H21 hc -0.01014 1.00790 H 1 1.000000 0.000000 0
+5 MAIN 1 CHX H22 hc -0.01014 1.00790 H 1 1.000000 0.000000 0
+6 MAIN 1 CHX C3 c3 0.02028 12.01070 C 6 1.000000 0.000000 0
+7 MAIN 1 CHX H31 hc -0.01014 1.00790 H 1 1.000000 0.000000 0
+8 MAIN 1 CHX H32 hc -0.01014 1.00790 H 1 1.000000 0.000000 0
+9 MAIN 1 CHX C4 c3 0.02028 12.01070 C 6 1.000000 0.000000 0
+10 MAIN 1 CHX H41 hc -0.01014 1.00790 H 1 1.000000 0.000000 0
+11 MAIN 1 CHX H42 hc -0.01014 1.00790 H 1 1.000000 0.000000 0
+12 MAIN 1 CHX C5 c3 0.02028 12.01070 C 6 1.000000 0.000000 0
+13 MAIN 1 CHX H51 hc -0.01014 1.00790 H 1 1.000000 0.000000 0
+14 MAIN 1 CHX H52 hc -0.01014 1.00790 H 1 1.000000 0.000000 0
+15 MAIN 1 CHX C6 c3 0.02028 12.01070 C 6 1.000000 0.000000 0
+16 MAIN 1 CHX H61 hc -0.01014 1.00790 H 1 1.000000 0.000000 0
+17 MAIN 1 CHX H62 hc -0.01014 1.00790 H 1 1.000000 0.000000 0
+
+!:positions ; frame 0
+! idx x y z [sx sy sz]
+0 -0.42599112 -0.35929320 0.35655500
+1 -1.01624424 -0.72957195 -0.50347826
+2 -0.54179774 -1.12578223 1.14873323
+3 1.04137452 -0.23088342 -0.03511225
+4 1.12957943 0.00701261 -1.11305842
+5 1.53920328 -1.21209989 0.09028237
+6 1.76939017 0.83531425 0.77498801
+7 1.72079910 1.81017924 0.24987721
+8 2.84619642 0.58857820 0.84406243
+9 1.17573802 0.98306172 2.16460859
+10 1.77465297 1.69714837 2.76171992
+11 1.24785607 0.01475657 2.69906908
+12 -0.27685708 1.44109308 2.10781038
+13 -0.33123797 2.54598209 2.15885618
+14 -0.80849776 1.07941130 3.00941320
+15 -0.99011676 0.96147512 0.84913012
+16 -0.89787879 1.72139798 0.04758561
+17 -2.07557052 0.86450816 1.04290559
+
+!:bonds
+! from1 to1 from2 to2 from3 to3 from4 to4
+0 1 0 2 3 5 3 4
+6 8 6 7 3 6 9 11
+9 10 6 9 12 14 12 13
+9 12 15 17 15 16 12 15
+0 3 0 15
+
+!:angles
+! a1 b1 c1 a2 b2 c2 a3 b3 c3
+1 0 2 5 3 4 8 6 7
+5 3 6 4 3 6 3 6 8
+3 6 7 11 9 10 8 6 9
+7 6 9 3 6 9 6 9 11
+6 9 10 14 12 13 11 9 12
+10 9 12 6 9 12 9 12 14
+9 12 13 17 15 16 14 12 15
+13 12 15 9 12 15 12 15 17
+12 15 16 1 0 3 2 0 3
+0 3 5 0 3 4 0 3 6
+1 0 15 2 0 15 3 0 15
+0 15 17 0 15 16 0 15 12
+
+!:dihedrals
+! a1 b1 c1 d1 a2 b2 c2 d2
+5 3 6 8 5 3 6 7
+4 3 6 8 4 3 6 7
+8 6 9 11 8 6 9 10
+7 6 9 11 7 6 9 10
+3 6 9 11 3 6 9 10
+11 9 12 14 11 9 12 13
+10 9 12 14 10 9 12 13
+6 9 12 14 6 9 12 13
+14 12 15 17 14 12 15 16
+13 12 15 17 13 12 15 16
+9 12 15 17 9 12 15 16
+1 0 3 5 1 0 3 4
+1 0 3 6 2 0 3 5
+2 0 3 4 2 0 3 6
+1 0 15 17 1 0 15 16
+1 0 15 12 2 0 15 17
+2 0 15 16 2 0 15 12
+3 0 15 17 3 0 15 16
+3 0 15 12 15 0 3 5
+15 0 3 4 15 0 3 6
+5 3 6 9 4 3 6 9
+0 3 6 8 0 3 6 7
+0 3 6 9 8 6 9 12
+7 6 9 12 3 6 9 12
+11 9 12 15 10 9 12 15
+6 9 12 15 14 12 15 0
+13 12 15 0 9 12 15 0
+
+!:md_parameters
+log_file (null)
+coord_file (null)
+vel_file (null)
+force_file (null)
+debug_file (null)
+debug_output_level 0
+step 0
+coord_output_freq 10
+energy_output_freq 10
+coord_frame 497
+timestep 1
+cutoff 9
+electro_cutoff 9
+pairlist_distance 10
+switch_distance 8
+temperature 300
+andersen_freq 50
+andersen_coupling 0.1
+random_seed 0
+dielectric 4.8
+gradient_convergence 1e-06
+coordinate_convergence 1e-08
+use_xplor_shift 1
+scale14_vdw 0.5
+scale14_elect 0.83
+relocate_center 1
+surface_probe_radius 0
+surface_tension -0.005
+surface_potential_freq 5
+use_graphite 0
+alchemical_lambda 0
+alchemical_delta_lambda 0.1
+
+!:parameters
+! type1 type2 k r0
+bond c3 hc 337.299999 1.092000 ![gaff] SOURCE3  2815    0.0040    0.0059
+bond c3 c3 303.100018 1.535000 ![gaff] SOURCE1 14664    0.0043    0.0048
+! type1 type2 type3 k a0
+angle hc c3 hc 39.400002 108.349996 ![gaff] SOURCE3 2380   0.7199   0.9006
+angle c3 c3 hc 46.400000 110.050002 ![gaff] SOURCE3 2092   0.5379   0.6991
+angle c3 c3 c3 63.200000 110.629995 ![gaff] SOURCE3  507   1.7605   2.7845
+! type1 type2 type3 type4 k periodicity phi0
+dihe hc c3 c3 hc 0.150000 3 0.000000 ![gaff] Junmei et al, 1999
+dihe c3 c3 c3 hc 0.160000 3 0.000000 ![gaff] Junmei et al, 1999
+dihe c3 c3 c3 c3 0.200000 1 180.000005 ![gaff] Junmei et al, 1999
+! type eps r_eq eps14 r_eq14 atomic_number weight
+vdw c3 0.109400 1.908000 0.109400 1.908000 6 12.010000 ![gaff] Sp3 C
+vdw hc 0.015700 1.487000 0.015700 1.487000 1 1.008000 ![gaff] H bonded to aliphatic carbon without electrwd. group
+
+!:velocity
+! idx vx vy vz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+9 0.00000000 0.00000000 0.00000000
+10 0.00000000 0.00000000 0.00000000
+11 0.00000000 0.00000000 0.00000000
+12 0.00000000 0.00000000 0.00000000
+13 0.00000000 0.00000000 0.00000000
+14 0.00000000 0.00000000 0.00000000
+15 0.00000000 0.00000000 0.00000000
+16 0.00000000 0.00000000 0.00000000
+17 0.00000000 0.00000000 0.00000000
+
+!:force
+! idx fx fy fz
+0 0.00000000 0.00000000 0.00000000
+1 0.00000000 0.00000000 0.00000000
+2 0.00000000 0.00000000 0.00000000
+3 0.00000000 0.00000000 0.00000000
+4 0.00000000 0.00000000 0.00000000
+5 0.00000000 0.00000000 0.00000000
+6 0.00000000 0.00000000 0.00000000
+7 0.00000000 0.00000000 0.00000000
+8 0.00000000 0.00000000 0.00000000
+9 0.00000000 0.00000000 0.00000000
+10 0.00000000 0.00000000 0.00000000
+11 0.00000000 0.00000000 0.00000000
+12 0.00000000 0.00000000 0.00000000
+13 0.00000000 0.00000000 0.00000000
+14 0.00000000 0.00000000 0.00000000
+15 0.00000000 0.00000000 0.00000000
+16 0.00000000 0.00000000 0.00000000
+17 0.00000000 0.00000000 0.00000000
+
+!:trackball
+! scale; trx try trz; theta_deg x y z
+0.598406
+-0.034843 -0.065720 -0.108705
+240.501785 -0.193498 0.932829 -0.303954
+
+!:view
+show_unit_cell 0
+show_periodic_box 1
+show_expanded_atoms 1
+show_ellipsoids 0
+show_hydrogens 1
+show_dummy_atoms 1
+show_rotation_center 0
+show_graphite_flag 0
+show_graphite 5
+show_periodic_image_flag 0
+show_periodic_image 0 0 0 0 0 0
+