GROMACS version: 2018. 4
GROMACS modification: Yes/No
I have a mdp file used with Kirk-Wood buff force filed. But, I want to change the parameters according to the CHARMM36. And can any one please tell me what parameters need to be changed? The parameters used in KBFF are given bellow.
integrator = md
; Start time and timestep in ps
**tinit = 0 **
**dt = 0.002 **
**nsteps = 5000000 **
; For exact run continuation or redoing part of a run
init_step = 0 ;update for exact continuations
; Part index is updated automatically on checkpointing (keeps files separate)
simulation-part = 1
; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 500
; 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 = -1
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol = 10
emstep = 0.01
; 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 = 500 ;1ns
nstvout = 0
nstfout = 0
; Output frequency for energies to log file and energy file
**nstlog = 500 **
nstcalcenergy = 100
**nstenergy = 500 **
; Output frequency and precision for .xtc file
nstxout-compressed = 0 ;10ps
compressed-x-precision = 1000
; This selects the subset of atoms for the compressed
; trajectory file. You can select multiple groups. By
; default, all atoms will be written.
compressed-x-grps = Protein
; Selection of energy groups
**energygrps = Protein Pb Cl SOL **
; NEIGHBORSEARCHING PARAMETERS
; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)
cutoff-scheme = Verlet
; nblist update frequency
nstlist = 10
; ns algorithm (simple or grid)
ns-type = Grid
; Periodic boundary conditions: xyz, no, xy
pbc = xyz
periodic-molecules = no
; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,
; a value of -1 means: use rlist
verlet-buffer-tolerance = 0.005
**; nblist cut-off **
rlist = 1.0
; long-range cut-off for switched potentials
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
coulomb-modifier = Potential-shift-Verlet
rcoulomb-switch = 0
rcoulomb = 1.0
; Relative dielectric constant for the medium and the reaction field
epsilon-r = 1
epsilon_rf = 1
; Method for doing Van der Waals
vdw-type = PME
vdw-modifier = Potential-shift-Verlet
**; cut-off lengths **
rvdw-switch = 0
rvdw = 1.0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; Separate 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-rtol-lj = 0.001
lj-pme-comb-rule = geometric
ewald_geometry = 3d
epsilon_surface = 0
; 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 = 1
; 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
gb-dielectric-offset = 0.009
sa-algorithm = Ace-approximation
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The value -1 will set default value for Still/HCT/OBC GB-models.
sa-surface-tension = -1
; OPTIONS FOR WEAK COUPLING ALGORITHMS
**; Temperature coupling **
**tcoupl = Nose-Hoover **
nsttcouple = -1
nh-chain-length = 10
print-nose-hoover-chain-variables = no
; Groups to couple separately
tc-grps = Protein Non-Protein
; Time constant (ps) and reference temperature (K)
**tau-t = 0.5 0.5 **
ref-t = 300.0 300.0
**; pressure coupling **
**Pcoupl = Parrinello-Rahman **
Pcoupltype = isotropic
nstpcouple = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
**tau-p = 2.5 **
compressibility = 4.5e-5
ref-p = 1
; Scaling of reference coordinates, No, All or COM
refcoord-scaling = No
; 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 = 300.0
gen-seed = 173529
**; OPTIONS FOR BONDS **
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 = 4
; 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 = no
**; ENFORCED ROTATION **
; Enforced rotation: No or Yes
rotation = no
; Group to display and/or manipulate in interactive MD session
**IMD-group = **
**; 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
; Free energy variables
free-energy = no
**couple-moltype = **
couple-lambda0 = vdw-q
couple-lambda1 = vdw-q
couple-intramol = no
init-lambda = -1
init-lambda-state = -1
delta-lambda = 0
nstdhdl = 50
**fep-lambdas = **
**mass-lambdas = **
**coul-lambdas = **
**vdw-lambdas = **
**bonded-lambdas = **
**restraint-lambdas = **
**temperature-lambdas = **
calc-lambda-neighbors = 1
**init-lambda-weights = **
dhdl-print-energy = no
sc-alpha = 0
sc-power = 1
sc-r-power = 6
sc-sigma = 0.3
sc-coul = no
separate-dhdl-file = yes
dhdl-derivatives = yes
dh_hist_size = 0
dh_hist_spacing = 0.1
; Non-equilibrium MD stuff
**acc-grps = **
**accelerate = **
**freezegrps = **
**freezedim = **
cos-acceleration = 0
**deform = **
; simulated tempering variables
simulated-tempering = no
simulated-tempering-scaling = geometric
sim-temp-low = 300
sim-temp-high = 300
**; Electric fields **
; Format is number of terms (int) and for all terms an amplitude (real)
; and a phase angle (real)
**E-x = **
; Time dependent (pulsed) electric field. Format is omega, time for pulse
; peak, and sigma (width) for pulse. Sigma = 0 removes pulse, leaving
; the field to be a cosine function.
**E-xt = **
**E-y = **
**E-yt = **
**E-z = **
**E-zt = **
; Ion/water position swapping for computational electrophysiology setups
; Swap positions along direction: no, X, Y, Z
swapcoords = no
adress = no
; User defined thingies
**user1-grps = **
**user2-grps = **
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0