9 |
|
MetallicEnergyUnitScaling 23.0605423 |
10 |
|
end Options |
11 |
|
|
12 |
+ |
|
13 |
|
begin AtomTypes |
14 |
|
//Name mass (amu) |
15 |
|
CH4 16.05 |
16 |
|
CH3 15.04 |
17 |
|
CH2 14.03 |
18 |
|
CH 13.02 |
19 |
< |
thCH3 15.04 |
20 |
< |
thCH2 14.03 |
21 |
< |
//thS 32.0655 |
19 |
> |
// CH3 (sp3) thiol/sulfide/disulfide |
20 |
> |
CH3S 15.04 |
21 |
> |
// CH2 (sp3) thiol/sulfide/disulfide |
22 |
> |
CH2S 14.03 |
23 |
> |
//CH (sp3) all other/thiol |
24 |
> |
CHS 13.02 |
25 |
> |
//C (sp3) all other/thiol |
26 |
> |
CS 12.0107 |
27 |
> |
// sulfone |
28 |
> |
SYZ 32.0655 |
29 |
> |
// O in sulfone |
30 |
> |
OY |
31 |
> |
// thiol S |
32 |
> |
SH 32.0655 |
33 |
> |
//Thiol H |
34 |
> |
HS 1.0079 |
35 |
> |
// Sulfoxide |
36 |
> |
SZ 32.0655 |
37 |
> |
// Sulfur in disulfide |
38 |
> |
SS 32.0655 |
39 |
> |
// Sulfur in aromatic (thiophene) |
40 |
> |
SP 32.0655 |
41 |
> |
// sp2 carbon in thiophene |
42 |
> |
CS 12.0107 |
43 |
> |
// Sulfur attached to gold |
44 |
> |
SAu 228.9807 |
45 |
> |
|
46 |
> |
//Water |
47 |
|
SSD 18.0153 |
48 |
|
SSD1 18.0153 |
49 |
|
SSD_E 18.0153 |
64 |
|
EP_TIP4P 0.0 |
65 |
|
EP_TIP4P-Ew 0.0 |
66 |
|
EP_TIP5P 0.0 |
67 |
+ |
|
68 |
+ |
//Standard Atoms |
69 |
|
C 12.0107 |
70 |
|
S 32.0655 |
71 |
|
Ni 58.710 |
100 |
|
O_TIP5P-E 0.178 3.097 |
101 |
|
O_SPCE 0.15532 3.16549 |
102 |
|
O_SPC 0.15532 3.16549 |
103 |
< |
CH4 0.279 3.73 |
104 |
< |
//CH3 0.185 3.75 |
105 |
< |
//CH2 0.0866 3.95 |
106 |
< |
CH 0.0189 4.68 |
107 |
< |
C 0.101745452544 3.35 |
108 |
< |
CH3 0.2146 3.76 |
109 |
< |
CH2 0.1127 3.96 |
110 |
< |
S 0.2504 4.45 |
103 |
> |
// From TraPPE-UA JPCB, 109, 24100 and JCPB 102,2569 |
104 |
> |
CH4 0.2941 3.73 |
105 |
> |
CH3 0.1947 3.75 |
106 |
> |
CH2 0.09140 3.95 |
107 |
> |
CH 0.0987 4.68 |
108 |
> |
CS 0.0009935 6.40 |
109 |
> |
CH3S 0.1947 3.75 |
110 |
> |
CH2S 0.09140 3.95 |
111 |
> |
CHS 0.0987 4.68 |
112 |
> |
S 0.3954 3.58 |
113 |
> |
SH 0.4610 3.62 |
114 |
> |
SS 0.3279 3.72 |
115 |
> |
SP 0.3576 3.60 |
116 |
|
end LennardJonesAtomTypes |
117 |
|
|
118 |
|
begin SCAtomTypes |
238 |
|
CH2 CH Harmonic 1.526 260 |
239 |
|
CH CH Harmonic 1.526 260 |
240 |
|
// fix the Kb for the thiol below: |
241 |
< |
S CH2 Harmonic 1.82 260 |
241 |
> |
S CH2 Harmonic 1.82 281 |
242 |
|
|
243 |
|
//Atom1 Atom2 Cubic b0 K3 K2 K1 K0 |
244 |
|
//V_Cubic = K3(b - b0)^3 + K2(b - b0)^2 + K1(b - b0) + K0 |
304 |
|
|
305 |
|
// All thiol torsions from Kautman and Klein (J. Phys. Chem. 1989, 91, 4994-5001) |
306 |
|
|
307 |
< |
S CH2 CH2 CH3 Polynomial 0 2.218 1 2.905 2 -3.136 3 -0.7313 4 6.272 5 -7.528 |
308 |
< |
S CH2 CH2 CH2 Polynomial 0 2.218 1 2.905 2 -3.136 3 -0.7313 4 6.272 5 -7.528 |
309 |
< |
S CH2 CH2 CH Polynomial 0 2.218 1 2.905 2 -3.136 3 -0.7313 4 6.272 5 -7.528 |
310 |
< |
S CH2 CH2 C Polynomial 0 2.218 1 2.905 2 -3.136 3 -0.7313 4 6.272 5 -7.528 |
307 |
> |
//S CH2 CH2 CH3 Polynomial 0 2.218 1 2.905 2 -3.136 3 -0.7313 4 6.272 5 -7.528 |
308 |
> |
//S CH2 CH2 CH2 Polynomial 0 2.218 1 2.905 2 -3.136 3 -0.7313 4 6.272 5 -7.528 |
309 |
> |
//S CH2 CH2 CH Polynomial 0 2.218 1 2.905 2 -3.136 3 -0.7313 4 6.272 5 -7.528 |
310 |
> |
//S CH2 CH2 C Polynomial 0 2.218 1 2.905 2 -3.136 3 -0.7313 4 6.272 5 -7.528 |
311 |
|
|
312 |
|
// All type 1 possibilities from Dubbeldam et al. (J. Phys. Chem. B 2004, 108, 12301-12313) |
313 |
|
|
314 |
< |
CH3 CH2 CH2 CH3 Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
315 |
< |
CH3 CH2 CH2 CH2 Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
316 |
< |
CH3 CH2 CH2 CH Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
317 |
< |
CH3 CH2 CH2 C Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
318 |
< |
CH2 CH2 CH2 CH2 Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
319 |
< |
CH2 CH2 CH2 CH Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
320 |
< |
CH2 CH2 CH2 C Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
321 |
< |
CH CH2 CH2 CH Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
322 |
< |
CH CH2 CH2 C Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
323 |
< |
C CH2 CH2 C Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
314 |
> |
//CH3 CH2 CH2 CH3 Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
315 |
> |
//CH3 CH2 CH2 CH2 Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
316 |
> |
//CH3 CH2 CH2 CH Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
317 |
> |
//CH3 CH2 CH2 C Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
318 |
> |
//CH2 CH2 CH2 CH2 Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
319 |
> |
//CH2 CH2 CH2 CH Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
320 |
> |
//CH2 CH2 CH2 C Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
321 |
> |
//CH CH2 CH2 CH Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
322 |
> |
//CH CH2 CH2 C Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
323 |
> |
//C CH2 CH2 C Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
324 |
|
|
325 |
|
// All type 2 possibilities: |
326 |
|
|
327 |
< |
H CH CH2 CH3 Polynomial 0 2.7167 1 8.665 2 0.82669 3 -12.92 4 -1.653 5 3.2712 |
328 |
< |
H CH CH2 CH2 Polynomial 0 2.7161 1 8.665 2 0.82669 3 -12.92 4 -1.653 5 3.2712 |
329 |
< |
H CH CH2 CH Polynomial 0 2.7161 1 8.665 2 0.82669 3 -12.92 4 -1.653 5 3.2712 |
330 |
< |
H CH CH2 C Polynomial 0 2.7161 1 8.665 2 0.82669 3 -12.92 4 -1.653 5 3.2712 |
327 |
> |
//H CH CH2 CH3 Polynomial 0 2.7167 1 8.665 2 0.82669 3 -12.92 4 -1.653 5 3.2712 |
328 |
> |
//H CH CH2 CH2 Polynomial 0 2.7161 1 8.665 2 0.82669 3 -12.92 4 -1.653 5 3.2712 |
329 |
> |
//H CH CH2 CH Polynomial 0 2.7161 1 8.665 2 0.82669 3 -12.92 4 -1.653 5 3.2712 |
330 |
> |
//H CH CH2 C Polynomial 0 2.7161 1 8.665 2 0.82669 3 -12.92 4 -1.653 5 3.2712 |
331 |
|
|
332 |
|
// All type 3 possibilities: |
333 |
|
|
334 |
< |
CH3 C CH2 CH3 Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
335 |
< |
CH3 C CH2 CH2 Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
336 |
< |
CH3 C CH2 CH Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
337 |
< |
CH3 C CH2 C Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
338 |
< |
CH2 C CH2 CH2 Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
339 |
< |
CH2 C CH2 CH Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
340 |
< |
CH2 C CH2 C Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
341 |
< |
CH C CH2 CH Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
342 |
< |
CH C CH2 C Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
343 |
< |
C C CH2 C Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
334 |
> |
//CH3 C CH2 CH3 Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
335 |
> |
//CH3 C CH2 CH2 Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
336 |
> |
//CH3 C CH2 CH Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
337 |
> |
//CH3 C CH2 C Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
338 |
> |
//CH2 C CH2 CH2 Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
339 |
> |
//CH2 C CH2 CH Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
340 |
> |
//CH2 C CH2 C Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
341 |
> |
//CH C CH2 CH Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
342 |
> |
//CH C CH2 C Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
343 |
> |
//C C CH2 C Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
344 |
|
|
345 |
|
// All type 4 possibilities: |
346 |
|
|
347 |
< |
CH3 C C CH3 Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
348 |
< |
CH3 C C CH2 Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
349 |
< |
CH3 C C CH Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
350 |
< |
CH3 C C C Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
351 |
< |
CH2 C C CH2 Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
352 |
< |
CH2 C C CH Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
353 |
< |
CH2 C C C Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
354 |
< |
CH C C CH Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
355 |
< |
CH C C C Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
356 |
< |
C C C C Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
347 |
> |
//CH3 C C CH3 Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
348 |
> |
//CH3 C C CH2 Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
349 |
> |
//CH3 C C CH Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
350 |
> |
//CH3 C C C Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
351 |
> |
//CH2 C C CH2 Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
352 |
> |
//CH2 C C CH Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
353 |
> |
//CH2 C C C Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
354 |
> |
//CH C C CH Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
355 |
> |
//CH C C C Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
356 |
> |
//C C C C Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
357 |
|
|
358 |
|
//All type 5 possibilities: |
359 |
|
|
360 |
< |
CH3 C CH H Polynomial 0 3.1301 1 9.390 2 0 3 -12.52 4 0 5 0 |
361 |
< |
CH2 C CH H Polynomial 0 3.1301 1 9.390 2 0 3 -12.52 4 0 5 0 |
362 |
< |
CH C CH H Polynomial 0 3.1301 1 9.390 2 0 3 -12.52 4 0 5 0 |
363 |
< |
C C CH H Polynomial 0 3.1301 1 9.390 2 0 3 -12.52 4 0 5 0 |
360 |
> |
//CH3 C CH H Polynomial 0 3.1301 1 9.390 2 0 3 -12.52 4 0 5 0 |
361 |
> |
//CH2 C CH H Polynomial 0 3.1301 1 9.390 2 0 3 -12.52 4 0 5 0 |
362 |
> |
//CH C CH H Polynomial 0 3.1301 1 9.390 2 0 3 -12.52 4 0 5 0 |
363 |
> |
//C C CH H Polynomial 0 3.1301 1 9.390 2 0 3 -12.52 4 0 5 0 |
364 |
|
|
365 |
|
//All type 6 possibilities: |
366 |
|
|
367 |
< |
H CH CH H Polynomial 0 2.1706 1 5.609 2 -1.804 3 -5.976 4 3.6089 5 -3.6089 |
367 |
> |
//H CH CH H Polynomial 0 2.1706 1 5.609 2 -1.804 3 -5.976 4 3.6089 5 -3.6089 |
368 |
|
|
369 |
|
//Cubic |
370 |
|
//Atom1 Atom2 Atom3 Atom4 Cubic k3 k2 k1 k0 ( all are kcal/mol ) |
371 |
|
//V_Cubic = k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0 |
372 |
|
//Cubic Examples |
373 |
< |
//CH3 CH2 CH2 CH3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
374 |
< |
//CH3 CH2 CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
375 |
< |
//CH3 CH CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
376 |
< |
//CH3 CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
377 |
< |
//CH3 CH2 CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
378 |
< |
//CH3 CH CH2 CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
379 |
< |
//CH3 CH CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
380 |
< |
//CH3 CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
381 |
< |
//CH3 CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
382 |
< |
//CH3 CH CH2 CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
383 |
< |
//CH3 CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
384 |
< |
//CH2 CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
385 |
< |
//CH2 CH2 CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
386 |
< |
//CH2 CH CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
387 |
< |
//CH2 CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
388 |
< |
//CH2 CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
389 |
< |
//CH2 CH CH2 CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
390 |
< |
//CH2 CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
391 |
< |
//CH CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
392 |
< |
//CH CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
393 |
< |
//CH CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
394 |
< |
//S CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
373 |
> |
CH3 CH2 CH2 CH3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
374 |
> |
CH3 CH2 CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
375 |
> |
CH3 CH CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
376 |
> |
CH3 CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
377 |
> |
CH3 CH2 CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
378 |
> |
CH3 CH CH2 CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
379 |
> |
CH3 CH CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
380 |
> |
CH3 CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
381 |
> |
CH3 CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
382 |
> |
CH3 CH CH2 CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
383 |
> |
CH3 CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
384 |
> |
CH2 CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
385 |
> |
CH2 CH2 CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
386 |
> |
CH2 CH CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
387 |
> |
CH2 CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
388 |
> |
CH2 CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
389 |
> |
CH2 CH CH2 CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
390 |
> |
CH2 CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
391 |
> |
CH CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
392 |
> |
CH CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
393 |
> |
CH CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
394 |
> |
S CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
395 |
|
|
396 |
+ |
//Opls |
397 |
+ |
//Atom1 Atom2 Atom3 Atom4 Opls v0 v1 v2 v3 |
398 |
+ |
//V_Opls = v0 + v1 / 2 * [1 + cos(phi)] + v2 / 2 * [1 - cos(2*phi)] + v3 / 2 * [1 + cos(3*phi)] |
399 |
+ |
//units for v_n: kcal / mol |
400 |
+ |
|
401 |
+ |
|
402 |
|
//Charmm |
403 |
|
//Atom1 Atom2 Atom3 Atom4 Charmm Kchi n delta [Kchi n delta] |
404 |
|
//V_Charmm = Kchi(1 + cos(n(chi) - delta)) |