[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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