[gmx-users] Problems with non-bonded interactions using OPLSAA
Mike Wykes
mikewykes at gmail.com
Thu Jul 2 19:01:28 CEST 2009
Dear all
I would like to simulate beta cyclodextrin in various organic
solvents with the OPLSAA FF for Carbohydrates (J Comput Chem 18:
1955-1970, 1997) but am having problems with the short range Coulomb
and LJ interactions.
This FF (and OPLS in general) does not assign LJ parameters to
hydrogen atoms in OH groups, relying on the repulsion between oxygens
to keep the hydrogen (charge +0.435 ) of one OH group getting too
close to the O (charge -0.7 ) of another.
However in MD simulations, the hydrogen of one OH group collides with
the O of another, and shortly after the system explodes.
Obviously, this could be a mistake of how I converted the parameters
in the paper into gromacs parameters, so I have checked this and found
no mistakes. Some of the parameters are taken from regular OPLS,
allowing me to check my conversion by comparing to the parameters in
gromacs/share/top/ffoplsaa*.itp files.
Out of curiosity I implemented the same forcefield in the tinker md
package and the O...H system was stable during MD, with no O..H
collisions. Comparing the energies of exactly the same geometry of
beta cyclodextrin with the same OPLS parameters shows identical bonded
interactions, but differences in the non-bonded interactions:
tinker(kcal/mol) gmx (kj/mol) gmx(kcal/mol)
difference
Total Potential energy 312 -1416.98 -338.67 650.67
Bond Stretching 23.32 97.58 23.32 0
Angle Bending 30.38 127.11 30.38 0
Torsional Angle 312.06 1305.64 312.06 0
Van der Waals 13.69 -119.03 -28.45 42.14
Charge-Charge -67.45 -2828.29 -675.98 608.52
In both cases the molecule was in the gas phase, all non-bonded
interactions being treated with a cutoff of 1.5 nm.
Any suggestions as to what could be going wrong in my gromacs
calculations would be much appreciated.
Please find my mdp, top and itp files below. I am using version 4.0.5.
Many thanks,
Mike
mdp file:
;
; File 'mdout.mdp' was generated
; By user: mwykes (7017)
; On host: node177
; At date: Wed Apr 8 14:39:36 2009
;
; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/hoe
include =
; e.g.: -DI_Want_Cookies -DMe_Too
define = -DFLEX_SPC
; RUN CONTROL PARAMETERS
integrator = steep
; Start time and timestep in ps
tinit = 0
dt = 0.0002
nsteps = 10
; For exact run continuation or redoing part of a run
; Part index is updated automatically on checkpointing (keeps files separate)
simulation_part = 1
init_step = 0
; mode for center of mass motion removal
comm-mode = LINEAR
; number of steps for center of mass motion removal
nstcomm = 1
; group(s) for center of mass motion removal
comm-grps =
; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric = 0
ld-seed = 1993
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol = 0.1
emstep = 0.1
; Max number of iterations in relax_shells
niter = 20
; Step size (ps^2) for minimization of flexible constraints
fcstep = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep = 1000
nbfgscorr = 10
; TEST PARTICLE INSERTION OPTIONS
rtpi = 0.05
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 1
nstvout = 0
nstfout = 0
; Output frequency for energies to log file and energy file
nstlog = 1
nstenergy = 1
; Output frequency and precision for xtc file
nstxtcout = 1
xtc-precision = 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps =
; Selection of energy groups
energygrps =
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 1
; ns algorithm (simple or grid)
nstype = simple
; Periodic boundary conditions: xyz, no, xy
pbc = no
periodic_molecules = no
; nblist cut-off
rlist = 1.5
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = Cut-off
rcoulomb-switch = 0
rcoulomb = 1.5
; Relative dielectric constant for the medium and the reaction field
epsilon_r = 1
epsilon_rf = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch = 0
rvdw = 1.5
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; Seperate tables between energy group pairs
energygrp_table =
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = no
; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = No
; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 2
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent = 80
; Salt concentration in M for Generalized Born models
gb_saltconc = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2.
sa_surface_tension = 2.092
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = nose-hoover
; Groups to couple separately
tc-grps =System
; Time constant (ps) and reference temperature (K)
;Use tau_t 0.01 for equilibration, 0.1-0.5 for data collection
tau_t = 0.1
ref_t = 300
; Pressure coupling
Pcoupl = no
Pcoupltype = Isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
; use 0.5-1 to equilibrate, use 1-5 to collect data
tau-p = 1
compressibility = 5.25e-5
ref-p = 1.0
; Scaling of reference coordinates, No, All or COM
refcoord_scaling = No
; Random seed for Andersen thermostat
andersen_seed = 815131
; OPTIONS FOR QMMM calculations
QMMM = no
; Groups treated Quantum Mechanically
QMMM-grps =
; QM method
QMmethod =
; QMMM scheme
QMMMscheme = normal
; QM basisset
QMbasis =
; QM charge
QMcharge =
; QM multiplicity
QMmult =
; Surface Hopping
SH =
; CAS space options
CASorbitals =
CASelectrons =
SAon =
SAoff =
SAsteps =
; Scale factor for MM charges
MMChargeScaleFactor = 1
; Optimization of QM subsystem
bOPT =
bTS =
; SIMULATED ANNEALING
; Type of annealing for each temperature group (no/single/periodic)
annealing =
; Number of time points to use for specifying annealing in each group
annealing_npoints =
; List of times at the annealing points for each group
annealing_time =
; Temp. at each annealing point, for each group.
annealing_temp =
; GENERATE VELOCITIES FOR STARTUP RUN
gen-vel = yes
gen-temp = 300
gen-seed = 173529
; OPTIONS FOR BONDS
constraints = none
;constraints = all-bonds
; Type of constraint algorithm
constraint-algorithm = Lincs
; Do not constrain the start configuration
continuation = no
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR = no
; Relative tolerance of shake
shake-tol = 0.0001
; Highest order in the expansion of the constraint coupling matrix
lincs-order = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter = 1
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle = 30
; Convert harmonic bonds to morse potentials
morse = no
; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions are excluded
energygrp_excl =
; WALLS
; Number of walls, type, atom types, densities and box-z scale factor for Ewald
nwall = 0
wall_type = 9-3
wall_r_linpot = -1
wall_atomtype =
wall_density =
wall_ewald_zfac = 3
; COM PULLING
; Pull type: no, umbrella, constraint or constant_force
pull = no
; NMR refinement stuff
; Distance restraints type: No, Simple or Ensemble
disre = No
; Force weighting of pairs in one distance restraint: Conservative or Equal
disre-weighting = Conservative
; Use sqrt of the time averaged times the instantaneous violation
disre-mixed = no
disre-fc = 1000
disre-tau = 0
; Output frequency for pair distances to energy file
nstdisreout = 100
; Orientation restraints: No or Yes
orire = no
; Orientation restraints force constant and tau for time averaging
orire-fc = 0
orire-tau = 0
orire-fitgrp =
; Output frequency for trace(SD) and S to energy file
nstorireout = 100
; Dihedral angle restraints: No or Yes
dihre = no
dihre_fc = 9999.0
; Free energy control stuff
free-energy = no
init-lambda = 0
delta-lambda = 0
sc-alpha = 0
sc-power = 0
sc-sigma = 0.3
couple-moltype =
couple-lambda0 = vdw-q
couple-lambda1 = vdw-q
couple-intramol = no
; Non-equilibrium MD stuff
acc-grps =
accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
deform =
; Electric fields
; Format is number of terms (int) and for all terms an amplitude (real)
; and a phase angle (real)
E-x =
E-xt =
E-y =
E-yt =
E-z =
E-zt =
; User defined thingies
user1-grps =
user2-grps =
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
Top file:
#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
BCD 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 opls_301 1 BCD CO1 1 0.300 12.000
2 opls_302 1 BCD HC2 1 0.100 1.008
3 opls_300 1 BCD CT3 2 0.205 12.000
4 opls_302 1 BCD HC4 2 0.060 1.008
5 opls_305 1 BCD OH25 3 -0.700 15.999
6 opls_303 1 BCD HO6 3 0.435 1.008
7 opls_300 1 BCD CT7 4 0.205 12.000
8 opls_302 1 BCD HC8 4 0.060 1.008
9 opls_305 1 BCD OH29 5 -0.700 15.999
10 opls_303 1 BCD HO10 5 0.435 1.008
11 opls_300 1 BCD CT11 6 0.205 12.000
12 opls_302 1 BCD HC12 6 0.060 1.008
13 opls_306 1 BCD OS13 7 -0.465 15.999
14 opls_300 1 BCD CT14 8 0.170 12.000
15 opls_302 1 BCD HC15 8 0.030 1.008
16 opls_300 1 BCD CT16 9 0.145 12.000
17 opls_302 1 BCD HC17 9 0.060 1.008
18 opls_302 1 BCD HC18 9 0.060 1.008
19 opls_304 1 BCD OH119 10 -0.683 15.999
20 opls_303 1 BCD HO20 10 0.418 1.008
21 opls_306 1 BCD OS21 11 -0.400 15.999
22 opls_301 1 BCD CO22 12 0.300 12.000
23 opls_302 1 BCD HC23 12 0.100 1.008
24 opls_300 1 BCD CT24 13 0.205 12.000
25 opls_302 1 BCD HC25 13 0.060 1.008
26 opls_305 1 BCD OH226 14 -0.700 15.999
27 opls_303 1 BCD HO27 14 0.435 1.008
28 opls_300 1 BCD CT28 15 0.205 12.000
29 opls_302 1 BCD HC29 15 0.060 1.008
30 opls_305 1 BCD OH230 16 -0.700 15.999
31 opls_303 1 BCD HO31 16 0.435 1.008
32 opls_300 1 BCD CT32 17 0.205 12.000
33 opls_302 1 BCD HC33 17 0.060 1.008
34 opls_306 1 BCD OS34 18 -0.465 15.999
35 opls_300 1 BCD CT35 19 0.170 12.000
36 opls_302 1 BCD HC36 19 0.030 1.008
37 opls_300 1 BCD CT37 20 0.145 12.000
38 opls_302 1 BCD HC38 20 0.060 1.008
39 opls_302 1 BCD HC39 20 0.060 1.008
40 opls_304 1 BCD OH140 21 -0.683 15.999
41 opls_303 1 BCD HO41 21 0.418 1.008
42 opls_306 1 BCD OS42 22 -0.400 15.999
43 opls_301 1 BCD CO43 23 0.300 12.000
44 opls_302 1 BCD HC44 23 0.100 1.008
45 opls_300 1 BCD CT45 24 0.205 12.000
46 opls_302 1 BCD HC46 24 0.060 1.008
47 opls_305 1 BCD OH247 25 -0.700 15.999
48 opls_303 1 BCD HO48 25 0.435 1.008
49 opls_300 1 BCD CT49 26 0.205 12.000
50 opls_302 1 BCD HC50 26 0.060 1.008
51 opls_305 1 BCD OH251 27 -0.700 15.999
52 opls_303 1 BCD HO52 27 0.435 1.008
53 opls_300 1 BCD CT53 28 0.205 12.000
54 opls_302 1 BCD HC54 28 0.060 1.008
55 opls_306 1 BCD OS55 29 -0.465 15.999
56 opls_300 1 BCD CT56 30 0.170 12.000
57 opls_302 1 BCD HC57 30 0.030 1.008
58 opls_300 1 BCD CT58 31 0.145 12.000
59 opls_302 1 BCD HC59 31 0.060 1.008
60 opls_302 1 BCD HC60 31 0.060 1.008
61 opls_304 1 BCD OH161 32 -0.683 15.999
62 opls_303 1 BCD HO62 32 0.418 1.008
63 opls_306 1 BCD OS63 33 -0.400 15.999
64 opls_301 1 BCD CO64 34 0.300 12.000
65 opls_302 1 BCD HC65 34 0.100 1.008
66 opls_300 1 BCD CT66 35 0.205 12.000
67 opls_302 1 BCD HC67 35 0.060 1.008
68 opls_305 1 BCD OH268 36 -0.700 15.999
69 opls_303 1 BCD HO69 36 0.435 1.008
70 opls_300 1 BCD CT70 37 0.205 12.000
71 opls_302 1 BCD HC71 37 0.060 1.008
72 opls_305 1 BCD OH272 38 -0.700 15.999
73 opls_303 1 BCD HO73 38 0.435 1.008
74 opls_300 1 BCD CT74 39 0.205 12.000
75 opls_302 1 BCD HC75 39 0.060 1.008
76 opls_306 1 BCD OS76 40 -0.465 15.999
77 opls_300 1 BCD CT77 41 0.170 12.000
78 opls_302 1 BCD HC78 41 0.030 1.008
79 opls_300 1 BCD CT79 42 0.145 12.000
80 opls_302 1 BCD HC80 42 0.060 1.008
81 opls_302 1 BCD HC81 42 0.060 1.008
82 opls_304 1 BCD OH182 43 -0.683 15.999
83 opls_303 1 BCD HO83 43 0.418 1.008
84 opls_306 1 BCD OS84 44 -0.400 15.999
85 opls_301 1 BCD CO85 45 0.300 12.000
86 opls_302 1 BCD HC86 45 0.100 1.008
87 opls_300 1 BCD CT87 46 0.205 12.000
88 opls_302 1 BCD HC88 46 0.060 1.008
89 opls_305 1 BCD OH289 47 -0.700 15.999
90 opls_303 1 BCD HO90 47 0.435 1.008
91 opls_300 1 BCD CT91 48 0.205 12.000
92 opls_302 1 BCD HC92 48 0.060 1.008
93 opls_305 1 BCD OH293 49 -0.700 15.999
94 opls_303 1 BCD HO94 49 0.435 1.008
95 opls_300 1 BCD CT95 50 0.205 12.000
96 opls_302 1 BCD HC96 50 0.060 1.008
97 opls_306 1 BCD OS97 51 -0.465 15.999
98 opls_300 1 BCD CT98 52 0.170 12.000
99 opls_302 1 BCD HC99 52 0.030 1.008
100 opls_300 1 BCD CT100 53 0.145 12.000
101 opls_302 1 BCD HC101 53 0.060 1.008
102 opls_302 1 BCD HC102 53 0.060 1.008
103 opls_304 1 BCD OH1103 54 -0.683 15.999
104 opls_303 1 BCD HO104 54 0.418 1.008
105 opls_306 1 BCD OS105 55 -0.400 15.999
106 opls_301 1 BCD CO106 56 0.300 12.000
107 opls_302 1 BCD HC107 56 0.100 1.008
108 opls_300 1 BCD CT108 57 0.205 12.000
109 opls_302 1 BCD HC109 57 0.060 1.008
110 opls_305 1 BCD OH2110 58 -0.700 15.999
111 opls_303 1 BCD HO111 58 0.435 1.008
112 opls_300 1 BCD CT112 59 0.205 12.000
113 opls_302 1 BCD HC113 59 0.060 1.008
114 opls_305 1 BCD OH2114 60 -0.700 15.999
115 opls_303 1 BCD HO115 60 0.435 1.008
116 opls_300 1 BCD CT116 61 0.205 12.000
117 opls_302 1 BCD HC117 61 0.060 1.008
118 opls_306 1 BCD OS118 62 -0.465 15.999
119 opls_300 1 BCD CT119 63 0.170 12.000
120 opls_302 1 BCD HC120 63 0.030 1.008
121 opls_300 1 BCD CT121 64 0.145 12.000
122 opls_302 1 BCD HC122 64 0.060 1.008
123 opls_302 1 BCD HC123 64 0.060 1.008
124 opls_304 1 BCD OH1124 65 -0.683 15.999
125 opls_303 1 BCD HO125 65 0.418 1.008
126 opls_306 1 BCD OS126 66 -0.400 15.999
127 opls_301 1 BCD CO127 67 0.300 12.000
128 opls_302 1 BCD HC128 67 0.100 1.008
129 opls_300 1 BCD CT129 68 0.205 12.000
130 opls_302 1 BCD HC130 68 0.060 1.008
131 opls_305 1 BCD OH2131 69 -0.700 15.999
132 opls_303 1 BCD HO132 69 0.435 1.008
133 opls_300 1 BCD CT133 70 0.205 12.000
134 opls_302 1 BCD HC134 70 0.060 1.008
135 opls_305 1 BCD OH2135 71 -0.700 15.999
136 opls_303 1 BCD HO136 71 0.435 1.008
137 opls_300 1 BCD CT137 72 0.205 12.000
138 opls_302 1 BCD HC138 72 0.060 1.008
139 opls_306 1 BCD OS139 73 -0.465 15.999
140 opls_300 1 BCD CT140 74 0.170 12.000
141 opls_302 1 BCD HC141 74 0.030 1.008
142 opls_300 1 BCD CT142 75 0.145 12.000
143 opls_302 1 BCD HC143 75 0.060 1.008
144 opls_302 1 BCD HC144 75 0.060 1.008
145 opls_304 1 BCD OH1145 76 -0.683 15.999
146 opls_303 1 BCD HO146 76 0.418 1.008
147 opls_306 1 BCD OS147 77 -0.400 15.999
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 3 1
1 21 1
1 139 1
3 4 1
3 5 1
3 7 1
5 6 1
7 8 1
7 9 1
7 11 1
9 10 1
11 12 1
11 13 1
11 14 1
13 22 1
14 15 1
14 16 1
14 21 1
16 17 1
16 18 1
16 19 1
19 20 1
22 23 1
22 24 1
22 42 1
24 25 1
24 26 1
24 28 1
26 27 1
28 29 1
28 30 1
28 32 1
30 31 1
32 33 1
32 34 1
32 35 1
34 43 1
35 36 1
35 37 1
35 42 1
37 38 1
37 39 1
37 40 1
40 41 1
43 44 1
43 45 1
43 63 1
45 46 1
45 47 1
45 49 1
47 48 1
49 50 1
49 51 1
49 53 1
51 52 1
53 54 1
53 55 1
53 56 1
55 64 1
56 57 1
56 58 1
56 63 1
58 59 1
58 60 1
58 61 1
61 62 1
64 65 1
64 66 1
64 84 1
66 67 1
66 68 1
66 70 1
68 69 1
70 71 1
70 72 1
70 74 1
72 73 1
74 75 1
74 76 1
74 77 1
76 85 1
77 78 1
77 79 1
77 84 1
79 80 1
79 81 1
79 82 1
82 83 1
85 86 1
85 87 1
85 105 1
87 88 1
87 89 1
87 91 1
89 90 1
91 92 1
91 93 1
91 95 1
93 94 1
95 96 1
95 97 1
95 98 1
97 106 1
98 99 1
98 100 1
98 105 1
100 101 1
100 102 1
100 103 1
103 104 1
106 107 1
106 108 1
106 126 1
108 109 1
108 110 1
108 112 1
110 111 1
112 113 1
112 114 1
112 116 1
114 115 1
116 117 1
116 118 1
116 119 1
118 127 1
119 120 1
119 121 1
119 126 1
121 122 1
121 123 1
121 124 1
124 125 1
127 128 1
127 129 1
127 147 1
129 130 1
129 131 1
129 133 1
131 132 1
133 134 1
133 135 1
133 137 1
135 136 1
137 138 1
137 139 1
137 140 1
140 141 1
140 142 1
140 147 1
142 143 1
142 144 1
142 145 1
145 146 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 1
2 1 21 1
2 1 139 1
3 1 21 1
3 1 139 1
21 1 139 1
1 3 4 1
1 3 5 1
1 3 7 1
4 3 5 1
4 3 7 1
5 3 7 1
3 5 6 1
3 7 8 1
3 7 9 1
3 7 11 1
8 7 9 1
8 7 11 1
9 7 11 1
7 9 10 1
7 11 12 1
7 11 13 1
7 11 14 1
12 11 13 1
12 11 14 1
13 11 14 1
11 13 22 1
11 14 15 1
11 14 16 1
11 14 21 1
15 14 16 1
15 14 21 1
16 14 21 1
14 16 17 1
14 16 18 1
14 16 19 1
17 16 18 1
17 16 19 1
18 16 19 1
16 19 20 1
1 21 14 1
13 22 23 1
13 22 24 1
13 22 42 1
23 22 24 1
23 22 42 1
24 22 42 1
22 24 25 1
22 24 26 1
22 24 28 1
25 24 26 1
25 24 28 1
26 24 28 1
24 26 27 1
24 28 29 1
24 28 30 1
24 28 32 1
29 28 30 1
29 28 32 1
30 28 32 1
28 30 31 1
28 32 33 1
28 32 34 1
28 32 35 1
33 32 34 1
33 32 35 1
34 32 35 1
32 34 43 1
32 35 36 1
32 35 37 1
32 35 42 1
36 35 37 1
36 35 42 1
37 35 42 1
35 37 38 1
35 37 39 1
35 37 40 1
38 37 39 1
38 37 40 1
39 37 40 1
37 40 41 1
22 42 35 1
34 43 44 1
34 43 45 1
34 43 63 1
44 43 45 1
44 43 63 1
45 43 63 1
43 45 46 1
43 45 47 1
43 45 49 1
46 45 47 1
46 45 49 1
47 45 49 1
45 47 48 1
45 49 50 1
45 49 51 1
45 49 53 1
50 49 51 1
50 49 53 1
51 49 53 1
49 51 52 1
49 53 54 1
49 53 55 1
49 53 56 1
54 53 55 1
54 53 56 1
55 53 56 1
53 55 64 1
53 56 57 1
53 56 58 1
53 56 63 1
57 56 58 1
57 56 63 1
58 56 63 1
56 58 59 1
56 58 60 1
56 58 61 1
59 58 60 1
59 58 61 1
60 58 61 1
58 61 62 1
43 63 56 1
55 64 65 1
55 64 66 1
55 64 84 1
65 64 66 1
65 64 84 1
66 64 84 1
64 66 67 1
64 66 68 1
64 66 70 1
67 66 68 1
67 66 70 1
68 66 70 1
66 68 69 1
66 70 71 1
66 70 72 1
66 70 74 1
71 70 72 1
71 70 74 1
72 70 74 1
70 72 73 1
70 74 75 1
70 74 76 1
70 74 77 1
75 74 76 1
75 74 77 1
76 74 77 1
74 76 85 1
74 77 78 1
74 77 79 1
74 77 84 1
78 77 79 1
78 77 84 1
79 77 84 1
77 79 80 1
77 79 81 1
77 79 82 1
80 79 81 1
80 79 82 1
81 79 82 1
79 82 83 1
64 84 77 1
76 85 86 1
76 85 87 1
76 85 105 1
86 85 87 1
86 85 105 1
87 85 105 1
85 87 88 1
85 87 89 1
85 87 91 1
88 87 89 1
88 87 91 1
89 87 91 1
87 89 90 1
87 91 92 1
87 91 93 1
87 91 95 1
92 91 93 1
92 91 95 1
93 91 95 1
91 93 94 1
91 95 96 1
91 95 97 1
91 95 98 1
96 95 97 1
96 95 98 1
97 95 98 1
95 97 106 1
95 98 99 1
95 98 100 1
95 98 105 1
99 98 100 1
99 98 105 1
100 98 105 1
98 100 101 1
98 100 102 1
98 100 103 1
101 100 102 1
101 100 103 1
102 100 103 1
100 103 104 1
85 105 98 1
97 106 107 1
97 106 108 1
97 106 126 1
107 106 108 1
107 106 126 1
108 106 126 1
106 108 109 1
106 108 110 1
106 108 112 1
109 108 110 1
109 108 112 1
110 108 112 1
108 110 111 1
108 112 113 1
108 112 114 1
108 112 116 1
113 112 114 1
113 112 116 1
114 112 116 1
112 114 115 1
112 116 117 1
112 116 118 1
112 116 119 1
117 116 118 1
117 116 119 1
118 116 119 1
116 118 127 1
116 119 120 1
116 119 121 1
116 119 126 1
120 119 121 1
120 119 126 1
121 119 126 1
119 121 122 1
119 121 123 1
119 121 124 1
122 121 123 1
122 121 124 1
123 121 124 1
121 124 125 1
106 126 119 1
118 127 128 1
118 127 129 1
118 127 147 1
128 127 129 1
128 127 147 1
129 127 147 1
127 129 130 1
127 129 131 1
127 129 133 1
130 129 131 1
130 129 133 1
131 129 133 1
129 131 132 1
129 133 134 1
129 133 135 1
129 133 137 1
134 133 135 1
134 133 137 1
135 133 137 1
133 135 136 1
133 137 138 1
133 137 139 1
133 137 140 1
138 137 139 1
138 137 140 1
139 137 140 1
1 139 137 1
137 140 141 1
137 140 142 1
137 140 147 1
141 140 142 1
141 140 147 1
142 140 147 1
140 142 143 1
140 142 144 1
140 142 145 1
143 142 144 1
143 142 145 1
144 142 145 1
142 145 146 1
127 147 140 1
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3 c4 c5
2 1 3 4 3
2 1 3 5 3
2 1 3 7 3
21 1 3 4 3
21 1 3 5 3
21 1 3 7 3
139 1 3 4 3
139 1 3 5 3
139 1 3 7 3
2 1 21 14 3
3 1 21 14 3
139 1 21 14 3
2 1 139 137 3
3 1 139 137 3
21 1 139 137 3
1 3 5 6 3
4 3 5 6 3
7 3 5 6 3
1 3 7 8 3
1 3 7 9 3
1 3 7 11 3
4 3 7 8 3
4 3 7 9 3
4 3 7 11 3
5 3 7 8 3
5 3 7 9 3
5 3 7 11 3
3 7 9 10 3
8 7 9 10 3
11 7 9 10 3
3 7 11 12 3
3 7 11 13 3
3 7 11 14 3
8 7 11 12 3
8 7 11 13 3
8 7 11 14 3
9 7 11 12 3
9 7 11 13 3
9 7 11 14 3
7 11 13 22 3
12 11 13 22 3
14 11 13 22 3
7 11 14 15 3
7 11 14 16 3
7 11 14 21 3
12 11 14 15 3
12 11 14 16 3
12 11 14 21 3
13 11 14 15 3
13 11 14 16 3
13 11 14 21 3
11 13 22 23 3
11 13 22 24 3
11 13 22 42 3
11 14 16 17 3
11 14 16 18 3
11 14 16 19 3
15 14 16 17 3
15 14 16 18 3
15 14 16 19 3
21 14 16 17 3
21 14 16 18 3
21 14 16 19 3
11 14 21 1 3
15 14 21 1 3
16 14 21 1 3
14 16 19 20 3
17 16 19 20 3
18 16 19 20 3
13 22 24 25 3
13 22 24 26 3
13 22 24 28 3
23 22 24 25 3
23 22 24 26 3
23 22 24 28 3
42 22 24 25 3
42 22 24 26 3
42 22 24 28 3
13 22 42 35 3
23 22 42 35 3
24 22 42 35 3
22 24 26 27 3
25 24 26 27 3
28 24 26 27 3
22 24 28 29 3
22 24 28 30 3
22 24 28 32 3
25 24 28 29 3
25 24 28 30 3
25 24 28 32 3
26 24 28 29 3
26 24 28 30 3
26 24 28 32 3
24 28 30 31 3
29 28 30 31 3
32 28 30 31 3
24 28 32 33 3
24 28 32 34 3
24 28 32 35 3
29 28 32 33 3
29 28 32 34 3
29 28 32 35 3
30 28 32 33 3
30 28 32 34 3
30 28 32 35 3
28 32 34 43 3
33 32 34 43 3
35 32 34 43 3
28 32 35 36 3
28 32 35 37 3
28 32 35 42 3
33 32 35 36 3
33 32 35 37 3
33 32 35 42 3
34 32 35 36 3
34 32 35 37 3
34 32 35 42 3
32 34 43 44 3
32 34 43 45 3
32 34 43 63 3
32 35 37 38 3
32 35 37 39 3
32 35 37 40 3
36 35 37 38 3
36 35 37 39 3
36 35 37 40 3
42 35 37 38 3
42 35 37 39 3
42 35 37 40 3
32 35 42 22 3
36 35 42 22 3
37 35 42 22 3
35 37 40 41 3
38 37 40 41 3
39 37 40 41 3
34 43 45 46 3
34 43 45 47 3
34 43 45 49 3
44 43 45 46 3
44 43 45 47 3
44 43 45 49 3
63 43 45 46 3
63 43 45 47 3
63 43 45 49 3
34 43 63 56 3
44 43 63 56 3
45 43 63 56 3
43 45 47 48 3
46 45 47 48 3
49 45 47 48 3
43 45 49 50 3
43 45 49 51 3
43 45 49 53 3
46 45 49 50 3
46 45 49 51 3
46 45 49 53 3
47 45 49 50 3
47 45 49 51 3
47 45 49 53 3
45 49 51 52 3
50 49 51 52 3
53 49 51 52 3
45 49 53 54 3
45 49 53 55 3
45 49 53 56 3
50 49 53 54 3
50 49 53 55 3
50 49 53 56 3
51 49 53 54 3
51 49 53 55 3
51 49 53 56 3
49 53 55 64 3
54 53 55 64 3
56 53 55 64 3
49 53 56 57 3
49 53 56 58 3
49 53 56 63 3
54 53 56 57 3
54 53 56 58 3
54 53 56 63 3
55 53 56 57 3
55 53 56 58 3
55 53 56 63 3
53 55 64 65 3
53 55 64 66 3
53 55 64 84 3
53 56 58 59 3
53 56 58 60 3
53 56 58 61 3
57 56 58 59 3
57 56 58 60 3
57 56 58 61 3
63 56 58 59 3
63 56 58 60 3
63 56 58 61 3
53 56 63 43 3
57 56 63 43 3
58 56 63 43 3
56 58 61 62 3
59 58 61 62 3
60 58 61 62 3
55 64 66 67 3
55 64 66 68 3
55 64 66 70 3
65 64 66 67 3
65 64 66 68 3
65 64 66 70 3
84 64 66 67 3
84 64 66 68 3
84 64 66 70 3
55 64 84 77 3
65 64 84 77 3
66 64 84 77 3
64 66 68 69 3
67 66 68 69 3
70 66 68 69 3
64 66 70 71 3
64 66 70 72 3
64 66 70 74 3
67 66 70 71 3
67 66 70 72 3
67 66 70 74 3
68 66 70 71 3
68 66 70 72 3
68 66 70 74 3
66 70 72 73 3
71 70 72 73 3
74 70 72 73 3
66 70 74 75 3
66 70 74 76 3
66 70 74 77 3
71 70 74 75 3
71 70 74 76 3
71 70 74 77 3
72 70 74 75 3
72 70 74 76 3
72 70 74 77 3
70 74 76 85 3
75 74 76 85 3
77 74 76 85 3
70 74 77 78 3
70 74 77 79 3
70 74 77 84 3
75 74 77 78 3
75 74 77 79 3
75 74 77 84 3
76 74 77 78 3
76 74 77 79 3
76 74 77 84 3
74 76 85 86 3
74 76 85 87 3
74 76 85 105 3
74 77 79 80 3
74 77 79 81 3
74 77 79 82 3
78 77 79 80 3
78 77 79 81 3
78 77 79 82 3
84 77 79 80 3
84 77 79 81 3
84 77 79 82 3
74 77 84 64 3
78 77 84 64 3
79 77 84 64 3
77 79 82 83 3
80 79 82 83 3
81 79 82 83 3
76 85 87 88 3
76 85 87 89 3
76 85 87 91 3
86 85 87 88 3
86 85 87 89 3
86 85 87 91 3
105 85 87 88 3
105 85 87 89 3
105 85 87 91 3
76 85 105 98 3
86 85 105 98 3
87 85 105 98 3
85 87 89 90 3
88 87 89 90 3
91 87 89 90 3
85 87 91 92 3
85 87 91 93 3
85 87 91 95 3
88 87 91 92 3
88 87 91 93 3
88 87 91 95 3
89 87 91 92 3
89 87 91 93 3
89 87 91 95 3
87 91 93 94 3
92 91 93 94 3
95 91 93 94 3
87 91 95 96 3
87 91 95 97 3
87 91 95 98 3
92 91 95 96 3
92 91 95 97 3
92 91 95 98 3
93 91 95 96 3
93 91 95 97 3
93 91 95 98 3
91 95 97 106 3
96 95 97 106 3
98 95 97 106 3
91 95 98 99 3
91 95 98 100 3
91 95 98 105 3
96 95 98 99 3
96 95 98 100 3
96 95 98 105 3
97 95 98 99 3
97 95 98 100 3
97 95 98 105 3
95 97 106 107 3
95 97 106 108 3
95 97 106 126 3
95 98 100 101 3
95 98 100 102 3
95 98 100 103 3
99 98 100 101 3
99 98 100 102 3
99 98 100 103 3
105 98 100 101 3
105 98 100 102 3
105 98 100 103 3
95 98 105 85 3
99 98 105 85 3
100 98 105 85 3
98 100 103 104 3
101 100 103 104 3
102 100 103 104 3
97 106 108 109 3
97 106 108 110 3
97 106 108 112 3
107 106 108 109 3
107 106 108 110 3
107 106 108 112 3
126 106 108 109 3
126 106 108 110 3
126 106 108 112 3
97 106 126 119 3
107 106 126 119 3
108 106 126 119 3
106 108 110 111 3
109 108 110 111 3
112 108 110 111 3
106 108 112 113 3
106 108 112 114 3
106 108 112 116 3
109 108 112 113 3
109 108 112 114 3
109 108 112 116 3
110 108 112 113 3
110 108 112 114 3
110 108 112 116 3
108 112 114 115 3
113 112 114 115 3
116 112 114 115 3
108 112 116 117 3
108 112 116 118 3
108 112 116 119 3
113 112 116 117 3
113 112 116 118 3
113 112 116 119 3
114 112 116 117 3
114 112 116 118 3
114 112 116 119 3
112 116 118 127 3
117 116 118 127 3
119 116 118 127 3
112 116 119 120 3
112 116 119 121 3
112 116 119 126 3
117 116 119 120 3
117 116 119 121 3
117 116 119 126 3
118 116 119 120 3
118 116 119 121 3
118 116 119 126 3
116 118 127 128 3
116 118 127 129 3
116 118 127 147 3
116 119 121 122 3
116 119 121 123 3
116 119 121 124 3
120 119 121 122 3
120 119 121 123 3
120 119 121 124 3
126 119 121 122 3
126 119 121 123 3
126 119 121 124 3
116 119 126 106 3
120 119 126 106 3
121 119 126 106 3
119 121 124 125 3
122 121 124 125 3
123 121 124 125 3
118 127 129 130 3
118 127 129 131 3
118 127 129 133 3
128 127 129 130 3
128 127 129 131 3
128 127 129 133 3
147 127 129 130 3
147 127 129 131 3
147 127 129 133 3
118 127 147 140 3
128 127 147 140 3
129 127 147 140 3
127 129 131 132 3
130 129 131 132 3
133 129 131 132 3
127 129 133 134 3
127 129 133 135 3
127 129 133 137 3
130 129 133 134 3
130 129 133 135 3
130 129 133 137 3
131 129 133 134 3
131 129 133 135 3
131 129 133 137 3
129 133 135 136 3
134 133 135 136 3
137 133 135 136 3
129 133 137 138 3
129 133 137 139 3
129 133 137 140 3
134 133 137 138 3
134 133 137 139 3
134 133 137 140 3
135 133 137 138 3
135 133 137 139 3
135 133 137 140 3
133 137 139 1 3
138 137 139 1 3
140 137 139 1 3
133 137 140 141 3
133 137 140 142 3
133 137 140 147 3
138 137 140 141 3
138 137 140 142 3
138 137 140 147 3
139 137 140 141 3
139 137 140 142 3
139 137 140 147 3
137 140 142 143 3
137 140 142 144 3
137 140 142 145 3
141 140 142 143 3
141 140 142 144 3
141 140 142 145 3
147 140 142 143 3
147 140 142 144 3
147 140 142 145 3
137 140 147 127 3
141 140 147 127 3
142 140 147 127 3
140 142 145 146 3
143 142 145 146 3
144 142 145 146 3
[ system ]
; Name
BCD
[ molecules ]
; Compound #mols
BCD 1
itp file:
#define _FF_OPLS
#define _FF_OPLSAA
; This force field uses a format that requires Gromacs 3.1.4 or later.
;
; References for the OPLS-AA force field:
;
; W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives,
; J. Am. Chem. Soc. 118, 11225-11236 (1996).
; W. L. Jorgensen and N. A. McDonald, Theochem 424, 145-155 (1998).
; W. L. Jorgensen and N. A. McDonald, J. Phys. Chem. B 102, 8049-8059 (1998).
; R. C. Rizzo and W. L. Jorgensen, J. Am. Chem. Soc. 121, 4827-4836 (1999).
; M. L. Price, D. Ostrovsky, and W. L. Jorgensen, J. Comp. Chem. (2001).
; E. K. Watkins and W. L. Jorgensen, J. Phys. Chem. A 105, 4118-4125 (2001).
; G. A. Kaminski, R.A. Friesner, J.Tirado-Rives and W.L. Jorgensen, J.
Phys. Chem. B 105, 6474 (2001).
;
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 3 yes 0.5 0.5
#include "ffBCD.new.itp"
itp parameter file:
[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name bond_type mass charge ptype sigma epsilon ;sigma
angstroms ;epsilon Kcal/mol
;example from gromacs opls file opls_001 C 6 12.011 0.5 A
3.75E-01 4.39E-01 ; SIG
;example from gromacs opls file opls_140 HC 1 1.008 0.06 A
2.50E-01 1.26E-01
opls_300 CT 6 12.000 0 A 3.50E-01 2.76E-01 ; 3.5 0.066
opls_301 CO 6 12.000 0 A 3.50E-01 2.76E-01 ; 3.5 0.066
opls_302 HC 1 1.008 0 A 2.50E-01 1.26E-01 ; 2.5 0.03
opls_303 HO 1 1.008 0 A 0.00E+00 0.00E+00 ; 0 0
opls_304 OH1 8 15.999 0 A 3.12E-01 7.11E-01 ; 3.12
0.17
opls_305 OH2 8 15.999 0 A 3.07E-01 7.11E-01 ; 3.07
0.17
opls_306 OS 8 15.999 0 A 2.90E-01 5.86E-01 ; 2.9 0.14
[ bondtypes ]
; i j func b0 kb
;example CT CT 1 0.1529 224262.4 ; CHARMM 22
parameter file
CT OS 1 0.141 267776.0 ; 320 1.41
CT OH1 1 0.141 267776.0 ; 320 1.41
CT OH2 1 0.141 267776.0 ; 320 1.41
CO OS 1 0.138 267776.0 ; 320 1.38
CO OH1 1 0.138 267776.0 ; 320 1.38
CO OH2 1 0.138 267776.0 ; 320 1.38
CT CT 1 0.1529 224262.4 ; 268 1.529
CT CO 1 0.1529 224262.4 ; 268 1.529
CT HC 1 0.109 284512.0 ; 340 1.09
CO HC 1 0.109 284512.0 ; 340 1.09
OH1 HO 1 0.0945 462750.4 ; 553 0.945
OH2 HO 1 0.0945 462750.4 ; 553 0.945
etc.etc..
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