16 |
|
CH3 15.04 |
17 |
|
CH2 14.03 |
18 |
|
CH 13.02 |
19 |
+ |
// Aromatic CH as in benzene |
20 |
+ |
CHar 13.02 |
21 |
+ |
// |
22 |
+ |
RCHar 12.0107 |
23 |
|
// CH3 (sp3) thiol/sulfide/disulfide |
24 |
|
CH3S 15.04 |
25 |
|
// CH2 (sp3) thiol/sulfide/disulfide |
49 |
|
// Sulfur attached to gold |
50 |
|
SAu 228.9807 |
51 |
|
|
52 |
+ |
|
53 |
|
//Water |
54 |
|
SSD 18.0153 |
55 |
|
SSD1 18.0153 |
116 |
|
CH3S 0.1947 3.75 |
117 |
|
CH2S 0.09140 3.95 |
118 |
|
CHS 0.0987 4.68 |
119 |
< |
S 0.3954 3.58 |
119 |
> |
// From CPC 177 2007 S-S distance on gold surfaces is 4.45 |
120 |
> |
S 0.3954 4.45 |
121 |
|
SH 0.4610 3.62 |
122 |
|
SS 0.3279 3.72 |
123 |
|
SP 0.3576 3.60 |
124 |
+ |
//From TraPPE-UA JPCB 104, 8008 |
125 |
+ |
CHar 0.1003 3.695 |
126 |
+ |
RCHar 0.04173 3.88 |
127 |
|
// ---- End From TraPPE-UA |
128 |
+ |
|
129 |
|
end LennardJonesAtomTypes |
130 |
|
|
131 |
|
begin SCAtomTypes |
159 |
|
// sigma epsilon |
160 |
|
Au CH3 LennardJones 3.54 0.2146 |
161 |
|
Au CH2 LennardJones 3.54 0.1749 |
162 |
< |
//Au SH LennardJones 4.45 9.180 |
163 |
< |
Au S LennardJones 4.45 9.180 |
162 |
> |
//Au SH LennardJones 2.40 8.465 |
163 |
> |
Au S LennardJones 2.40 8.465 |
164 |
|
|
165 |
|
//Shifted Morse |
166 |
|
// r0 D0 beta0 |
302 |
|
CH3 CH2 CH Harmonic 114.0 124.19 |
303 |
|
|
304 |
|
|
295 |
– |
|
305 |
|
//UreyBradley |
306 |
|
//Atom1 Atom2 Atom3 UreyBradley Theta0 Ktheta S0 Kub |
307 |
|
//V_UreyBradleyBend = Ktheta(Theta - Theta0)^2 + Kub(S - S0)^2 |
454 |
|
CH2 CH2 C S Trappe 0.0 0.0 0.0 0.91658 |
455 |
|
CH CH2 C S Trappe 0.0 0.0 0.0 0.91658 |
456 |
|
CH3 CG S H Trappe 0.0 0.0 0.0 0.79480 |
457 |
+ |
//From TraPPE-UA JPCB 104, 8008 |
458 |
|
|
459 |
|
//Charmm |
460 |
|
//Atom1 Atom2 Atom3 Atom4 Charmm Kchi n delta [Kchi n delta] |