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**