Commit 7b7e1694 authored by eric pellegrini's avatar eric pellegrini
Browse files

repopulate MDANSE

parent 5a2bf9e8
SPCE box
units kJ
molecular types 1
spce water
nummols 256
atoms 3
OW 16.0000 -0.82000 1 0 0d.a
HW 1.0000 0.41000 1 0 0.h.
HW 1.0000 0.41000 1 0 0.h.
constraints 3
1 2 1.000
1 3 1.000
2 3 1.633
finish
vdW 3
OW OW 12-6 0.26330E+07 2617.0 1.0000 1.0000 1.0000
OW HW 12-6 0.00000E+00 0.00000E+00 1.0000 1.0000 1.0000
HW HW 12-6 0.00000E+00 0.00000E+00 1.0000 1.0000 1.0000
close
Automatic FIELD created for 1 molecule of Cumene
units kJ
molecules 1
Cumene
nummols 1
atoms 21
CB 12.0110 -0.1150 1 0
CB 12.0110 -0.1150 1 0
CB 12.0110 -0.1150 1 0
CB 12.0110 -0.1150 1 0
CS 12.0110 0.0000 1 0
CB 12.0110 -0.1150 1 0
C3 12.0110 -0.0600 1 0
C1 12.0110 -0.1800 1 0
C1 12.0110 -0.1800 1 0
HR 1.0080 0.0600 1 0
HR 1.0080 0.0600 1 0
HR 1.0080 0.0600 1 0
HR 1.0080 0.0600 1 0
HR 1.0080 0.0600 1 0
HR 1.0080 0.0600 1 0
HB 1.0080 0.1150 1 0
HB 1.0080 0.1150 1 0
HB 1.0080 0.1150 1 0
HB 1.0080 0.1150 1 0
HB 1.0080 0.1150 1 0
HR 1.0080 0.0600 1 0
bonds 21
harm 7 8 2594.0801 1.526
harm 7 9 2594.0801 1.526
harm 5 7 2652.6560 1.520
harm 4 5 3924.5920 1.400
harm 5 6 3924.5920 1.400
harm 1 2 3924.5920 1.400
harm 1 6 3924.5920 1.400
harm 2 3 3924.5920 1.400
harm 3 4 3924.5920 1.400
harm 1 19 3071.0559 1.080
harm 2 18 3071.0559 1.080
harm 3 17 3071.0559 1.080
harm 4 16 3071.0559 1.080
harm 6 20 3071.0559 1.080
harm 8 13 2845.1201 1.090
harm 8 14 2845.1201 1.090
harm 8 15 2845.1201 1.090
harm 9 10 2845.1201 1.090
harm 9 11 2845.1201 1.090
harm 9 12 2845.1201 1.090
harm 7 21 2845.1201 1.090
angles 36
harm 1 2 3 527.1840 120.000
harm 2 1 6 527.1840 120.000
harm 2 3 4 527.1840 120.000
harm 1 6 5 527.1840 120.000
harm 3 4 5 527.1840 120.000
harm 4 5 6 527.1840 120.000
harm 4 5 7 585.7600 120.000
harm 6 5 7 585.7600 120.000
harm 1 2 18 292.8800 120.000
harm 1 6 20 292.8800 120.000
harm 2 1 19 292.8800 120.000
harm 2 3 17 292.8800 120.000
harm 3 2 18 292.8800 120.000
harm 3 4 16 292.8800 120.000
harm 4 3 17 292.8800 120.000
harm 6 1 19 292.8800 120.000
harm 5 4 16 292.8800 120.000
harm 5 6 20 292.8800 120.000
harm 5 7 8 527.1840 114.000
harm 5 7 9 527.1840 114.000
harm 8 7 9 334.7200 109.500
harm 5 7 21 418.4000 109.500
harm 8 7 21 418.4000 109.500
harm 9 7 21 418.4000 109.500
harm 7 8 13 418.4000 109.500
harm 7 8 14 418.4000 109.500
harm 7 8 15 418.4000 109.500
harm 7 9 10 418.4000 109.500
harm 7 9 11 418.4000 109.500
harm 7 9 12 418.4000 109.500
harm 10 9 11 585.7600 109.500
harm 10 9 12 585.7600 109.500
harm 11 9 12 585.7600 109.500
harm 13 8 14 585.7600 109.500
harm 13 8 15 585.7600 109.500
harm 14 8 15 585.7600 109.500
dihedrals 48
cos 1 2 3 4 60.6680 180.0000 2.0000 0.50 0.50
cos 3 2 1 6 60.6680 180.0000 2.0000 0.50 0.50
cos 1 6 5 4 60.6680 180.0000 2.0000 0.50 0.50
cos 3 4 5 6 60.6680 180.0000 2.0000 0.50 0.50
cos 2 1 6 5 60.6680 180.0000 2.0000 0.50 0.50
cos 2 3 4 5 60.6680 180.0000 2.0000 0.50 0.50
cos 1 2 3 17 60.6680 180.0000 2.0000 0.50 0.50
cos 2 1 6 20 60.6680 180.0000 2.0000 0.50 0.50
cos 2 3 4 16 60.6680 180.0000 2.0000 0.50 0.50
cos 3 2 1 19 60.6680 180.0000 2.0000 0.50 0.50
cos 4 3 2 18 60.6680 180.0000 2.0000 0.50 0.50
cos 6 1 2 18 60.6680 180.0000 2.0000 0.50 0.50
cos 5 4 3 17 60.6680 180.0000 2.0000 0.50 0.50
cos 5 6 1 19 60.6680 180.0000 2.0000 0.50 0.50
cos 4 5 6 20 60.6680 180.0000 2.0000 0.50 0.50
cos 6 5 4 16 60.6680 180.0000 2.0000 0.50 0.50
cos 16 4 3 17 60.6680 180.0000 2.0000 0.50 0.50
cos 17 3 2 18 60.6680 180.0000 2.0000 0.50 0.50
cos 18 2 1 19 60.6680 180.0000 2.0000 0.50 0.50
cos 19 1 6 20 60.6680 180.0000 2.0000 0.50 0.50
cos 1 6 5 7 60.6680 180.0000 2.0000 0.50 0.50
cos 3 4 5 7 60.6680 180.0000 2.0000 0.50 0.50
cos 7 5 4 16 60.6680 180.0000 2.0000 0.50 0.50
cos 7 5 6 20 60.6680 180.0000 2.0000 0.50 0.50
cos 4 5 7 8 0.0000 0.0000 2.0000 0.50 0.50
cos 4 5 7 9 0.0000 0.0000 2.0000 0.50 0.50
cos 6 5 7 8 0.0000 0.0000 2.0000 0.50 0.50
cos 6 5 7 9 0.0000 0.0000 2.0000 0.50 0.50
cos 4 5 7 21 0.0000 0.0000 2.0000 0.50 0.50
cos 6 5 7 21 0.0000 0.0000 2.0000 0.50 0.50
cos 5 7 8 13 5.8576 0.0000 3.0000 0.50 0.50
cos 5 7 8 14 5.8576 0.0000 3.0000 0.50 0.50
cos 5 7 8 15 5.8576 0.0000 3.0000 0.50 0.50
cos 5 7 9 10 5.8576 0.0000 3.0000 0.50 0.50
cos 5 7 9 11 5.8576 0.0000 3.0000 0.50 0.50
cos 5 7 9 12 5.8576 0.0000 3.0000 0.50 0.50
cos 10 9 7 21 5.8576 0.0000 3.0000 0.50 0.50
cos 11 9 7 21 5.8576 0.0000 3.0000 0.50 0.50
cos 12 9 7 21 5.8576 0.0000 3.0000 0.50 0.50
cos 13 8 7 21 5.8576 0.0000 3.0000 0.50 0.50
cos 14 8 7 21 5.8576 0.0000 3.0000 0.50 0.50
cos 15 8 7 21 5.8576 0.0000 3.0000 0.50 0.50
cos 8 7 9 10 5.8576 0.0000 3.0000 0.50 0.50
cos 8 7 9 11 5.8576 0.0000 3.0000 0.50 0.50
cos 8 7 9 12 5.8576 0.0000 3.0000 0.50 0.50
cos 9 7 8 13 5.8576 0.0000 3.0000 0.50 0.50
cos 9 7 8 14 5.8576 0.0000 3.0000 0.50 0.50
cos 9 7 8 15 5.8576 0.0000 3.0000 0.50 0.50
finish
vdw 21
HB HB lj 0.125520 2.420000
HB HR lj 0.125520 2.460000
HB CB lj 0.191735 2.985000
HB C3 lj 0.186176 2.960000
HB C1 lj 0.186176 2.960000
HB CS lj 0.191735 2.985000
HR HR lj 0.125520 2.500000
HR CB lj 0.191735 3.025000
HR C3 lj 0.186176 3.000000
HR C1 lj 0.186176 3.000000
HR CS lj 0.191735 3.025000
CB CB lj 0.292880 3.550000
CB C3 lj 0.284389 3.525000
CB C1 lj 0.284389 3.525000
CB CS lj 0.292880 3.550000
C3 C3 lj 0.276144 3.500000
C3 C1 lj 0.276144 3.500000
C3 CS lj 0.284389 3.525000
C1 C1 lj 0.276144 3.500000
C1 CS lj 0.284389 3.525000
CS CS lj 0.292880 3.550000
close
Automatic FIELD created for 1 molecule of felodipine
units kJ
molecules 1
felodipine
nummols 108
atoms 44
Cl 35.4530 -0.743 1 0
Cl 35.4530 -0.654 1 0
O_ 15.9940 -0.510 1 0
O 15.9940 -0.574 1 0
O_ 15.9940 -0.615 1 0
O 15.9940 -0.577 1 0
N 14.0070 -0.486 1 0
C= 12.0110 0.102 1 0
C= 12.0110 0.064 1 0
C 12.0110 -0.109 1 0
C= 12.0110 0.045 1 0
C= 12.0110 0.144 1 0
Cp 12.0110 0.041 1 0
Cp 12.0110 -0.125 1 0
Cp 12.0110 -0.116 1 0
Cp 12.0110 -0.067 1 0
Cp 12.0110 0.256 1 0
Cp 12.0110 0.310 1 0
C 12.0110 -0.349 1 0
C_ 12.0110 0.633 1 0
C 12.0110 0.045 1 0
C 12.0110 -0.360 1 0
C_ 12.0110 0.570 1 0
C 12.0110 -0.062 1 0
C 12.0110 -0.320 1 0
Hn 1.0080 0.337 1 0
H 1.0080 0.215 1 0
H 1.0080 0.158 1 0
H 1.0080 0.180 1 0
H 1.0080 0.170 1 0
H 1.0080 0.155 1 0
H 1.0080 0.169 1 0
H 1.0080 0.168 1 0
H 1.0080 0.176 1 0
H 1.0080 0.185 1 0
H 1.0080 0.203 1 0
H 1.0080 0.167 1 0
H 1.0080 0.198 1 0
H 1.0080 0.170 1 0
H 1.0080 0.190 1 0
H 1.0080 0.140 1 0
H 1.0080 0.170 1 0
H 1.0080 0.155 1 0
H 1.0080 0.151 1 0
bonds 45
mors 8 9 685.3392 1.330 2.000
mors 11 12 685.3392 1.330 2.000
mors 21 22 368.1920 1.526 1.915
mors 7 8 292.8800 1.420 2.000
mors 7 12 292.8800 1.420 2.000
mors 14 28 485.3440 1.080 1.77
mors 15 29 485.3440 1.080 1.77
mors 16 30 485.3440 1.080 1.77
mors 13 14 502.0800 1.340 2.000
mors 13 18 502.0800 1.340 2.000
mors 14 15 502.0800 1.340 2.000
mors 15 16 502.0800 1.340 2.000
mors 16 17 502.0800 1.340 2.000
mors 17 18 502.0800 1.340 2.000
mors 10 13 317.9840 1.510 1.93
mors 9 20 337.6488 1.500 2.000
mors 11 23 337.6488 1.500 2.000
mors 10 27 454.3824 1.105 1.771
mors 19 31 454.3824 1.105 1.771
mors 19 32 454.3824 1.105 1.771
mors 19 33 454.3824 1.105 1.771
mors 21 34 454.3824 1.105 1.771
mors 21 35 454.3824 1.105 1.771
mors 22 36 454.3824 1.105 1.771
mors 22 37 454.3824 1.105 1.771
mors 22 38 454.3824 1.105 1.771
mors 24 39 454.3824 1.105 1.771
mors 24 40 454.3824 1.105 1.771
mors 24 41 454.3824 1.105 1.771
mors 25 42 454.3824 1.105 1.771
mors 25 43 454.3824 1.105 1.771
mors 25 44 454.3824 1.105 1.771
mors 4 21 285.7672 1.425 2.000
mors 6 24 285.7672 1.425 2.000
mors 4 20 418.4000 1.370 2.000
mors 6 23 418.4000 1.370 2.000
mors 3 20 606.6800 1.230 2.06
mors 5 23 606.6800 1.230 2.06
mors 8 19 337.6488 1.500 2.000
mors 9 10 337.6488 1.500 2.000
mors 10 11 337.6488 1.500 2.000
mors 12 25 337.6488 1.500 2.000
mors 1 17 328.4440 1.761 2.000
mors 2 18 328.4440 1.761 2.000
mors 7 26 389.1120 1.026 2.280
angles 77
harm 31 19 32 330.5360 106.400
harm 31 19 33 330.5360 106.400
harm 32 19 33 330.5360 106.400
harm 34 21 35 330.5360 106.400
harm 36 22 37 330.5360 106.400
harm 36 22 38 330.5360 106.400
harm 37 22 38 330.5360 106.400
harm 39 24 40 330.5360 106.400
harm 39 24 41 330.5360 106.400
harm 40 24 41 330.5360 106.400
harm 42 25 43 330.5360 106.400
harm 42 25 44 330.5360 106.400
harm 43 25 44 330.5360 106.400
harm 21 22 36 371.5392 110.000
harm 21 22 37 371.5392 110.000
harm 21 22 38 371.5392 110.000
harm 22 21 34 371.5392 110.000
harm 22 21 35 371.5392 110.000
harm 13 14 28 309.6160 120.000
harm 14 15 29 309.6160 120.000
harm 15 14 28 309.6160 120.000
harm 15 16 30 309.6160 120.000
harm 16 15 29 309.6160 120.000
harm 17 16 30 309.6160 120.000
harm 13 14 15 753.1200 120.000
harm 13 18 17 753.1200 120.000
harm 14 13 18 753.1200 120.000
harm 14 15 16 753.1200 120.000
harm 15 16 17 753.1200 120.000
harm 16 17 18 753.1200 120.000
harm 13 10 27 371.5392 110.000
harm 10 13 14 369.8656 120.000
harm 10 13 18 369.8656 120.000
harm 8 9 20 302.9216 122.300
harm 12 11 23 302.9216 122.300
harm 8 9 10 302.9216 122.300
harm 9 8 19 302.9216 122.300
harm 10 11 12 302.9216 122.300
harm 11 12 25 302.9216 122.300
harm 8 19 31 371.5392 110.000
harm 8 19 32 371.5392 110.000
harm 8 19 33 371.5392 110.000
harm 9 10 27 371.5392 110.000
harm 11 10 27 371.5392 110.000
harm 12 25 42 371.5392 110.000
harm 12 25 43 371.5392 110.000
harm 12 25 44 371.5392 110.000
harm 3 20 9 418.4000 120.000
harm 5 23 11 418.4000 120.000
harm 1 17 16 711.2800 120.000
harm 1 17 18 711.2800 120.000
harm 2 18 13 711.2800 120.000
harm 2 18 17 711.2800 120.000
harm 20 4 21 502.0800 109.500
harm 23 6 24 502.0800 109.500
harm 3 20 4 1213.3600 123.000
harm 5 23 6 1213.3600 123.000
harm 4 20 9 418.4000 120.000
harm 6 23 11 418.4000 120.000
harm 10 9 20 418.4000 120.000
harm 10 11 23 418.4000 120.000
harm 4 21 22 585.7600 109.500
harm 4 21 34 476.9760 109.500
harm 4 21 35 476.9760 109.500
harm 6 24 39 476.9760 109.500
harm 6 24 40 476.9760 109.500
harm 6 24 41 476.9760 109.500
harm 7 8 9 753.1200 120.000
harm 7 12 11 753.1200 120.000
harm 7 8 19 418.4000 109.500
harm 7 12 25 418.4000 109.500
harm 8 7 12 628.4368 114.000
harm 8 7 26 293.7168 122.000
harm 12 7 26 293.7168 122.000
harm 9 10 11 389.9488 110.500
harm 9 10 13 389.9488 110.500
harm 11 10 13 389.9488 110.500
dihedrals 97
cos 34 21 22 36 5.9517 0.0000 3.0000 1.00 1.00
cos 34 21 22 37 5.9517 0.0000 3.0000 1.00 1.00
cos 34 21 22 38 5.9517 0.0000 3.0000 1.00 1.00
cos 35 21 22 36 5.9517 0.0000 3.0000 1.00 1.00
cos 35 21 22 37 5.9517 0.0000 3.0000 1.00 1.00
cos 35 21 22 38 5.9517 0.0000 3.0000 1.00 1.00
cos 4 21 22 36 5.9517 0.0000 3.0000 1.00 1.00
cos 4 21 22 37 5.9517 0.0000 3.0000 1.00 1.00
cos 4 21 22 38 5.9517 0.0000 3.0000 1.00 1.00
cos 20 4 21 22 1.6318 0.0000 3.0000 1.00 1.00
cos 20 4 21 34 1.6318 0.0000 3.0000 1.00 1.00
cos 20 4 21 35 1.6318 0.0000 3.0000 1.00 1.00
cos 23 6 24 39 1.6318 0.0000 3.0000 1.00 1.00
cos 23 6 24 40 1.6318 0.0000 3.0000 1.00 1.00
cos 23 6 24 41 1.6318 0.0000 3.0000 1.00 1.00
cos 9 20 4 21 18.8280 180.0000 2.0000 1.00 1.00
cos 11 23 6 24 18.8280 180.0000 2.0000 1.00 1.00
cos 3 20 4 21 18.8280 180.0000 2.0000 1.00 1.00
cos 5 23 6 24 18.8280 180.0000 2.0000 1.00 1.00
cos 13 14 15 16 50.2080 180.0000 2.0000 1.00 1.00
cos 13 18 17 16 50.2080 180.0000 2.0000 1.00 1.00
cos 14 13 18 17 50.2080 180.0000 2.0000 1.00 1.00
cos 14 15 16 17 50.2080 180.0000 2.0000 1.00 1.00
cos 15 14 13 18 50.2080 180.0000 2.0000 1.00 1.00
cos 15 16 17 18 50.2080 180.0000 2.0000 1.00 1.00
cos 10 13 14 15 50.2080 180.0000 2.0000 1.00 1.00
cos 10 13 18 17 50.2080 180.0000 2.0000 1.00 1.00
cos 13 14 15 29 50.2080 180.0000 2.0000 1.00 1.00
cos 14 15 16 30 50.2080 180.0000 2.0000 1.00 1.00
cos 16 15 14 28 50.2080 180.0000 2.0000 1.00 1.00
cos 17 16 15 29 50.2080 180.0000 2.0000 1.00 1.00
cos 18 13 14 28 50.2080 180.0000 2.0000 1.00 1.00
cos 18 17 16 30 50.2080 180.0000 2.0000 1.00 1.00
cos 28 14 15 29 50.2080 180.0000 2.0000 1.00 1.00
cos 29 15 16 30 50.2080 180.0000 2.0000 1.00 1.00
cos 1 17 16 30 50.2080 180.0000 2.0000 1.00 1.00
cos 1 17 18 2 50.2080 180.0000 2.0000 1.00 1.00
cos 1 17 16 15 50.2080 180.0000 2.0000 1.00 1.00
cos 1 17 18 13 50.2080 180.0000 2.0000 1.00 1.00
cos 2 18 13 14 50.2080 180.0000 2.0000 1.00 1.00
cos 2 18 17 16 50.2080 180.0000 2.0000 1.00 1.00
cos 10 13 14 28 50.2080 180.0000 2.0000 1.00 1.00
cos 2 18 13 10 50.2080 180.0000 2.0000 1.00 1.00
cos 14 13 10 27 0.0000 0.0000 2.0000 1.00 1.00
cos 18 13 10 27 0.0000 0.0000 2.0000 1.00 1.00
cos 9 10 13 14 0.0000 0.0000 2.0000 1.00 1.00
cos 9 10 13 18 0.0000 0.0000 2.0000 1.00 1.00
cos 11 10 13 14 0.0000 0.0000 2.0000 1.00 1.00
cos 11 10 13 18 0.0000 0.0000 2.0000 1.00 1.00
cos 10 9 8 19 68.1992 180.0000 2.0000 1.00 1.00
cos 10 11 12 25 68.1992 180.0000 2.0000 1.00 1.00
cos 7 8 9 10 68.1992 180.0000 2.0000 1.00 1.00
cos 7 12 11 10 68.1992 180.0000 2.0000 1.00 1.00
cos 7 8 9 20 68.1992 180.0000 2.0000 1.00 1.00
cos 7 12 11 23 68.1992 180.0000 2.0000 1.00 1.00
cos 19 8 9 20 68.1992 180.0000 2.0000 1.00 1.00
cos 23 11 12 25 68.1992 180.0000 2.0000 1.00 1.00
cos 8 9 10 13 5.2969 0.0000 3.0000 1.00 1.00
cos 12 11 10 13 5.2969 0.0000 3.0000 1.00 1.00
cos 20 9 10 27 5.2969 0.0000 3.0000 1.00 1.00
cos 23 11 10 27 5.2969 0.0000 3.0000 1.00 1.00
cos 8 9 10 27 5.2969 0.0000 3.0000 1.00 1.00
cos 9 8 19 31 5.2969 0.0000 3.0000 1.00 1.00
cos 9 8 19 32 5.2969 0.0000 3.0000 1.00 1.00
cos 9 8 19 33 5.2969 0.0000 3.0000 1.00 1.00
cos 11 12 25 42 5.2969 0.0000 3.0000 1.00 1.00
cos 11 12 25 43 5.2969 0.0000 3.0000 1.00 1.00
cos 11 12 25 44 5.2969 0.0000 3.0000 1.00 1.00
cos 12 11 10 27 5.2969 0.0000 3.0000 1.00 1.00
cos 9 10 11 23 5.2969 0.0000 3.0000 1.00 1.00
cos 11 10 9 20 5.2969 0.0000 3.0000 1.00 1.00
cos 8 9 10 11 5.2969 0.0000 3.0000 1.00 1.00
cos 9 10 11 12 5.2969 0.0000 3.0000 1.00 1.00
cos 7 8 19 31 5.2969 0.0000 3.0000 1.00 1.00
cos 7 8 19 32 5.2969 0.0000 3.0000 1.00 1.00
cos 7 8 19 33 5.2969 0.0000 3.0000 1.00 1.00
cos 7 12 25 42 5.2969 0.0000 3.0000 1.00 1.00
cos 7 12 25 43 5.2969 0.0000 3.0000 1.00 1.00
cos 7 12 25 44 5.2969 0.0000 3.0000 1.00 1.00
cos 13 10 9 20 5.2969 0.0000 3.0000 1.00 1.00
cos 13 10 11 23 5.2969 0.0000 3.0000 1.00 1.00
cos 3 20 9 8 7.5312 180.0000 2.0000 1.00 1.00
cos 5 23 11 12 7.5312 180.0000 2.0000 1.00 1.00
cos 3 20 9 10 7.5312 180.0000 2.0000 1.00 1.00
cos 5 23 11 10 7.5312 180.0000 2.0000 1.00 1.00
cos 4 20 9 8 7.5312 180.0000 2.0000 1.00 1.00
cos 6 23 11 12 7.5312 180.0000 2.0000 1.00 1.00
cos 4 20 9 10 7.5312 180.0000 2.0000 1.00 1.00
cos 6 23 11 10 7.5312 180.0000 2.0000 1.00 1.00
cos 8 7 12 11 41.8400 180.0000 2.0000 1.00 1.00
cos 9 8 7 12 41.8400 180.0000 2.0000 1.00 1.00
cos 8 7 12 25 41.8400 180.0000 2.0000 1.00 1.00
cos 12 7 8 19 41.8400 180.0000 2.0000 1.00 1.00
cos 9 8 7 26 41.8400 180.0000 2.0000 1.00 1.00
cos 11 12 7 26 41.8400 180.0000 2.0000 1.00 1.00
cos 19 8 7 26 41.8400 180.0000 2.0000 1.00 1.00
cos 25 12 7 26 41.8400 180.0000 2.0000 1.00 1.00
finish
vdw 55
C C lj 0.163176 3.875410
C C_ lj 0.317874 3.744002
C C= lj 0.317874 3.744002
C Cp lj 0.317874 3.744002
C H lj 0.161070 3.081337
C Hn lj 0.161070 3.081337
C N lj 0.337662 3.683572
C O lj 0.394540 3.329093
C O_ lj 0.394540 3.329093
C Cl lj 0.217202 3.702309
C_ C_ lj 0.619232 3.617050
C_ C= lj 0.619232 3.617050
C_ Cp lj 0.619232 3.617050
C_ H lj 0.313772 2.976855
C_ Hn lj 0.313772 2.976855
C_ N lj 0.657780 3.558669
C_ O lj 0.768582 3.216209
C_ O_ lj 0.768582 3.216209
C_ Cl lj 0.423118 3.576771
C= C= lj 0.619232 3.617050
C= Cp lj 0.619232 3.617050
C= H lj 0.313772 2.976855
C= Hn lj 0.313772 2.976855
C= N lj 0.657780 3.558669
C= O lj 0.768582 3.216209
C= O_ lj 0.768582 3.216209
C= Cl lj 0.423118 3.576771
Cp Cp lj 0.619232 3.617050
Cp H lj 0.313772 2.976855
Cp Hn lj 0.313772 2.976855
Cp N lj 0.657780 3.558669
Cp O lj 0.768582 3.216209
Cp O_ lj 0.768582 3.216209
Cp Cl lj 0.423118 3.576771
H H lj 0.158992 2.449970
H Hn lj 0.158992 2.449970
H N lj 0.333305 2.928807
H O lj 0.389449 2.646960
H O_ lj 0.389449 2.646960
H Cl lj 0.214399 2.943705
Hn Hn lj 0.158992 2.449970
Hn N lj 0.333305 2.928807
Hn O lj 0.389449 2.646960
Hn O_ lj 0.389449 2.646960
Hn Cl lj 0.214399 2.943705
N N lj 0.698728 3.501230
N O lj 0.816427 3.164298
N O_ lj 0.816427 3.164298
N Cl lj 0.449458 3.519040
O O lj 0.953952 2.859790
O O_ lj 0.953952 2.859790
O Cl lj 0.525168 3.180394
O_ O_ lj 0.953952 2.859790
O_ Cl lj 0.525168 3.180394
Cl Cl lj 0.289114 3.536940
close
methanol
units kJ
molecules 1
methanol
nummols 1000
atoms 6
CT 12.0110 0.1450 1 0
OH 15.9990 -0.6830 1 1
HO 1.0080 0.4180 1 0
HC 1.0080 0.0400 1 0
HC 1.0080 0.0400 1 0
HC 1.0080 0.0400 1 0
constraints 5
1 2 1.410
1 4 1.090
1 5 1.090
1 6 1.090
2 3 0.945
angles 7
harm 4 1 5 138.0720 107.800
harm 4 1 6 138.0720 107.800
harm 5 1 6 138.0720 107.800
harm 1 2 3 230.1200 108.500
harm 2 1 4 146.4400 109.500
harm 2 1 5 146.4400 109.500
harm 2 1 6 146.4400 109.500
dihedrals 3
cos3 3 2 1 4 0.0000 0.0000 1.8828 0.50 0.50
cos3 3 2 1 5 0.0000 0.0000 1.8828 0.50 0.50
cos3 3 2 1 6 0.0000 0.0000 1.8828 0.50 0.50
finish
vdw 10
CT CT lj 0.276144 3.500000
CT OH lj 0.443188 3.304542
CT HO lj 0.000000 0.000000
CT HC lj 0.186176 2.958040
OH OH lj 0.711280 3.120000
OH HO lj 0.000000 0.000000
OH HC lj 0.298797 2.792848
HO HO lj 0.000000 0.000000
HO HC lj 0.000000 0.000000
HC HC lj 0.125520 2.500000
close
TIP4P/2005 heavy water model
UNITS kJ
MOLECULES 1
TIP4P2005 water
NUMMOLS 4000
ATOMS 4
OW 15.999 0.0000 1 0 1
HW 2.014 0.5564 2 0 1
OM 0.000 -1.1128 1 0 1
RIGID BODIES 1
4 1 2 3 4
FINISH
VDW 1
OW OW lj 0.7749 3.1589
CLOSE
!From Abascal (2005):
!
! V = 4E*((s/r)^12-(s/r)^6) with s = 3.1589 A
! E = 93.2 K = 0.77490787 kJ/mol
!
!Water geometry: d(OH) = 0.9572 A, angle(HOH) = 104.52, d(OM) = 0.1546 A
TIP4P/2005 heavy water model
UNITS kJ
MOLECULES 1
TIP4P2005 water
NUMMOLS 4000
ATOMS 4
OW 15.999 0.0000 1 0 1
HW 2.014 0.5564 2 0 1
OM 0.000 -1.1128 1 0 1
RIGID BODIES 1
4 1 2 3 4
FINISH
VDW 1
OW OW lj 0.7749 3.1589
CLOSE
!From Abascal (2005):
!
! V = 4E*((s/r)^12-(s/r)^6) with s = 3.1589 A
! E = 93.2 K = 0.77490787 kJ/mol
!
!Water geometry: d(OH) = 0.9572 A, angle(HOH) = 104.52, d(OM) = 0.1546 A
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
# MDANSE
MDANSE (Molecular Dynamics Analysis for Neutron Scattering Experiments) is a python library/application for analysis molecular dynamics simulation data
This is nMoldyn-3.0.12, an interactive program for the
analysis of Molecular Dynamics trajectories. This program is
copyrighted but free to use for anyone under the CeCILL license,
see the file LICENSE for details.
nMoldyn should work with all major variants of Unix, including Linux
and MacOSX and Windows. There is little system-specific code in nMoldyn
itself, so porting nMoldyn to other systems should be straightforward.