; Preprocessing------------------------------------------------------------------------------------------------------------------------------------------- title = Energy Minimization ; redundant,so whatever comes to your mind cpp = /usr/bin/cpp ; your preprocessor ;include = /usr/local/gromacs/share/gromacs/top ; directories to include in your topology ;define = ; for defines in your topology file ; ; Run Control--------------------------------------------------------------------------------------------------------------------------------------------- integrator = md ; what you wanna do. md (moleculardynamics),steep (energyminimization), sd, md, cg, l-bfgs, nm, tpi,... tinit = 0 ; starting time for your run dt = 0.00333 ; time step for the integration nsteps = 30000 ; maximum number of steps to integrate ;init_step = ; the starting step {t=tinit +dt*(init_step +i)} comm_mode = None ; removal of center of mass movement ;nstcomm = ; frequency of that removal ;comm_grps = ; what groups are considered for removal ; ; Langevin Dynamics--------------------------------------------------------------------------------------------------------------------------------------- ;bd_fric = ; brownian dynamics friction coefficient ;ld_seed = ; used to initialize random generator for thermal noise for stochastic and Brownian dynamics ; ; Energy Minimization------------------------------------------------------------------------------------------------------------------------------------- ;emtol = 1 ; the minimization is converged when the maximum force is smaller than this value ;emstep = 0.01 ; initial step-size ;nstcgsteep = ; frequency of performing 1 steepest descent step while doing conjugate gradient energy minimization ;nbfgscorr = ; Number of correction steps to use for L-BFGS minimization. A higher number is more accurate, but slower ; ; Shell Molecular Dynamics-------------------------------------------------------------------------------------------------------------------------------- ;emtol = ; the minimization is converged when the maximum force is smaller than this value. shell-md: < 1 , em < 10 ;niter = ; maximum number of iterations for optimizing the shell positions and the flexible constraints ;fcstep = ; the step size for optimizing the flexible constraints ; ; Output Control------------------------------------------------------------------------------------------------------------------------------------------ nstxout = 10000 ; frequency to write coordinates to output trajectory file, the last coordinates are always written nstvout = 10000 ; frequency to write velocities to output trajectory, the last velocities are always written ;nstfout = ; frequency to write forces to output trajectory ;nstlog = 5000 ; frequency to write energies to log file, the last energies are always written ;nstenergy = 250 ; frequency to write energies to energy file, the last energies are always written ;nstxtcout = 250 ; frequency to write coordinates to xtc trajectory ;xtc_percision = ; precision to write to xtc trajectory ;xtc_grps = Protein ; group(s) to write to xtc trajectory, default the whole system is written (if nstxtcout is larger than zero) ;energygrps = Protein SOL ; group(s) to write to energy file ; ; Neighbor Searching-------------------------------------------------------------------------------------------------------------------------------------- nstlist = 5 ; Frequency to update the neighbor list. When this is 0, the neighbor list is made only once ns_type = grid ; grid or simple (grid for large systems) pbc = xyz ; periodic boundary conditions, xyz (every direction), no (no pbc) rlist = 1.75 ; cut-off distance for the short-range neighbor list ; ; Electrostatics------------------------------------------------------------------------------------------------------------------------------------------ ;coulombtype = cut-off ; other: Ewald, PME, PPPM, Reaction-Field, Generalized-RF, RF-nec, Shift, Encad-Shift, Switch, User, PME-User ;rcoulomb_switch = ; where to start switching the Coulomb potential ;rcoulomb = 1.4 ; distance for the Coulomb cut-off ;epsilon_r = ; The relative dielectric constant. A value of 0 means infinity ;epsilon_rf = ; The relative dielectric constant of the reaction field. A value of 0 means infinity ; ; VdW----------------------------------------------------------------------------------------------------------------------------------------------------- vdwtype = Cut-off ; Cut-off, Shift, Switch, Encad-Shift, User ;rvdw_switch = ; where to start switching the LJ potential rvdw = 1.75 ; distance for the LJ or Buckingham cut-off ;DispCorr = ; Dispersion Correction : no, EnerPress, Ener ; ; Tables-------------------------------------------------------------------------------------------------------------------------------------------------- ;table-extension = ; Extension of the non-bonded potential lookup tables beyond the largest cut-off distance ;energygrp_table = ; When user tables are used for electrostatics and/or VdW ; ; Ewald--------------------------------------------------------------------------------------------------------------------------------------------------- ;fourierspacing = ; The maximum grid spacing for the FFT grid when using PPPM or PME ;fourier_nx = ; Highest magnitude of wave vectors in reciprocal space when using Ewald ;pme_order = ; Interpolation order for PME ;ewald_rtol = ; The relative strength of the Ewald-shifted direct potential at the cutoff is given by ewald_rtol ;ewald_geometry = ; The geometry to use for Ewald summations ;epsilon_surface = ; This controls the dipole correction to the Ewald summation in 3d ;optimize_fft = ; Calculate the optimal FFT plan for the grid at startup : yes, no ; ; Temperature Coupling------------------------------------------------------------------------------------------------------------------------------------ tcoupl = Berendsen ; no, Berendsen, Nose-Hoover tc-grps = ETH ; groups to couple separately to temperature bath tau_t = 0.00333 ; time constant for coupling (one for each group in tc_grps), 0 means no temperature coupling ref_t = 183 ; reference temperature for coupling (one for each group in tc_grps) ; ; Pressure Coupling--------------------------------------------------------------------------------------------------------------------------------------- ;Pcoupl = Berendsen ; no, Berendson, Parinello-Rahman ;pcoupltype = ; isotropic, semiisotropic, anisotropic, surface-tension ;tau_p = 1.0 ; time constant for coupling ;compressibility = 4.5e-5 ; compressibility (NOTE: this is now really in bar-1) For water at 1 atm and 300 K the compressibility is 4.5e-5 ;ref_p = 1.0 ; reference pressure for coupling ; ; Simulated Annealing------------------------------------------------------------------------------------------------------------------------------------- ;annealing = single ; no, single, periodic ;annealing_npoints = 4 ; A list with the number of annealing reference/control points used for each temperature group ;annealing_time = 0 18 26 83 ; List of times at the annealing reference/control points for each group ;annealing_temp = 238 238 183 183 ; List of temperatures at the annealing reference/control points for each group ; ; Example: Assume you have two temperature groups, set the group selections to annealing = single periodic, the number of points of each group to ; annealing_npoints = 3 4, the times to annealing_time = 0 3 6 0 2 4 6 and finally temperatures to annealing_temp = 298 280 270 298 320 320 298. The ; first group will be coupled to 298K at 0ps, but the reference temperature will drop linearly to reach 280K at 3ps, and then linearly between 280K ; and 270K from 3ps to 6ps. After this is stays constant, at 270K. The second group is coupled to 298K at 0ps, it increases linearly to 320K at 2ps, ; where it stays constant until 4ps. Between 4ps and 6ps it decreases to 298K, and then it starts over with the same pattern again, i.e. rising ; linearly from 298K to 320K between 6ps and 8ps. Check the summary printed by grompp if you are unsure. ; ; Velocity Generation------------------------------------------------------------------------------------------------------------------------------------- ;gen_vel = yes ; Generate velocities according to a Maxwell distribution at temperature gen_temp [K], yes or no ;gen_temp = 183 ; temperature for Maxwell distribution ;gen_seed = 100000 ; used to initialize random generator for random velocities ; ; Bonds--------------------------------------------------------------------------------------------------------------------------------------------------- constraints = none ; none, hbonds, all-bonds, h-angles, all-angles constraint_algorithm = lincs ; lincs, shake unconstrained_start = no ; no, yes, apply constraints to the start configuration and reset shells ;shake_tol = ; relative tolerance for shake ;lincs_order = ; Highest order in the expansion of the constraint coupling matrix ;lincs_iter = ; Number of iterations to correct for rotational lengthening in Lincs ;lincs_warnangle = ; maximum angle that a bond can rotate before Lincs will complain ;morse = ; yes, no, bonds are represented by a Morse potential ; ; Energy Group Exclusions--------------------------------------------------------------------------------------------------------------------------------- ;energygrp_excl = ; Pairs of energy groups for which all non-bonded interactions are excluded ; ; NMR Refinement------------------------------------------------------------------------------------------------------------------------------------------ ;disre = ; no, simple, ensemble, distance restraints ;disre_weighting = ; conservative, equal ;disre_mixed = ; no, yes ;disre_fc = ; force constant for distance restraints, which is multiplied by a (possibly) different factor for each restraint ;disre_tau = ; time constant for distance restraints running average ;nstdisreout = ; frequency to write the running time averaged and instantaneous distances of all atom pairs involved in restraints ;orire = ; no, yes, orientation restraints ;orire_fc = ; force constant for orientation restraints ;orire_tau = ; time constant for orientation restraints running average ;orire_fitgrp = ; fit group for orientation restraining, for a protein backbone is a good choice ;nstorireout = ; frequency to write the running time averaged and instantaneous orientations ; ; Free Energy Perturbation-------------------------------------------------------------------------------------------------------------------------------- ;free_energy = ; no, yes, Interpolate between topology A to topology B ;init_lambda = ; starting value for lambda ;delta_lambda = ; increment per time step for lambda ;sc_alpha = ; the soft-core parameter, a value of 0 results in linear interpolation of the LJ and Coulomb interactions ;sc_power = ; the power for lambda in the soft-core function, only the values 1 and 2 are supported ;sc_sigma = ; the soft-core sigma for particles which have a C6 or C12 parameter equal to zero ; ; Non-Eqilibrium MD--------------------------------------------------------------------------------------------------------------------------------------- ;acc_grps = ; groups for constant acceleration ;accelerate = ; acceleration for acc_grps; x, y and z for each group ;freezegrps = ; Groups that are to be frozen ;freezedim = ; dimensions for which groups in freezegrps should be frozen ;cos_acceleration = ; the amplitude of the acceleration profile for calculating the viscosity ;deform = ; The velocities of deformation for the box elements ; ; Electric Field------------------------------------------------------------------------------------------------------------------------------------------ ;E_x = ; If you want to use an electric field in a direction, enter 3 numbers after the appropriate E_*, the first number ;E_y = ; the number of cosines, only 1 is implemented (with frequency 0)so enter 1, the second number: the strength of the ;E_z = ; electric field in V nm-1, the third number: the phase of the cosine you can enter any number here ;E_xt = ; not implemented yet ;E_yt = ; not implemented yet ;E_zt = ; not implemented yet ; ; Mixed Quantum/Classical Molecular Dynamics-------------------------------------------------------------------------------------------------------------- ;QMMM = ; no, yes, Do a QM/MM simulation ;QMMM-grps = ; groups to be descibed at the QM level ;QMMMscheme = ; normal, ONIOM ;QMmethod = ; Method used to compute the energy and gradients on the QM atoms ;QMbasis = ; Basisset used to expand the electronic wavefuntion ;QMcharge = ; The total charge in e of the QMMM-grps ;QMmult = ; The multiplicity of the QMMM-grps ;CASorbitals = ; The number of orbitals to be included in the active space when doing a CASSCF computation ;CASelectrons = ; The number of electrons to be included in the active space when doing a CASSCF computation ;SH = ; no, yes, Do a QM/MM MD simulation on the excited state-potential energy surface