From: Alexey Shvetsov Date: Tue, 11 Oct 2011 22:09:49 +0000 (+0400) Subject: Updated grompp.mdp for tutor/water X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=e8e8d5c12dfc432562ddc5829d5a4c959811c9aa;p=alexxy%2Fgromacs.git Updated grompp.mdp for tutor/water Updated grompp.mdp for tutor water that works with current gromacs Issue #802 Change-Id: I3a80fa15ea08b25dd817b743331fa278aefb0d15 Signed-off-by: Alexey Shvetsov --- diff --git a/share/tutor/water/grompp.mdp b/share/tutor/water/grompp.mdp index 4ae6b561b0..47cc901537 100644 --- a/share/tutor/water/grompp.mdp +++ b/share/tutor/water/grompp.mdp @@ -1,14 +1,15 @@ ; ; File 'mdout.mdp' was generated -; By user: spoel (291) -; On host: chagall -; At date: Mon Dec 15 13:13:06 2003 +; By user: alexxy (1000) +; On host: x201 +; At date: Wed Oct 12 02:06:35 2011 ; ; VARIOUS PREPROCESSING OPTIONS -title = Yo -cpp = /usr/bin/cpp +; Preprocessor information: use cpp syntax. +; e.g.: -I/home/joe/doe -I/home/mary/roe include = +; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) define = ; RUN CONTROL PARAMETERS @@ -19,16 +20,17 @@ dt = 0.002 nsteps = 10000 ; For exact run continuation or redoing part of a run init_step = 0 +; 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 = 1 +nstcomm = 10 ; group(s) for center of mass motion removal comm-grps = ; LANGEVIN DYNAMICS OPTIONS -; Temperature, friction coefficient (amu/ps) and random seed -bd-temp = 300 +; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 @@ -38,26 +40,28 @@ emtol = 100 emstep = 0.01 ; Max number of iterations in relax_shells niter = 20 -; Step size (1/ps^2) for minimization of flexible constraints +; 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 = 0 nstvout = 0 nstfout = 0 -; Checkpointing helps you continue after crashes -nstcheckpoint = 1000 ; Output frequency for energies to log file and energy file nstlog = 50 +nstcalcenergy = -1 nstenergy = 50 -; Output frequency and precision for xtc file +; Output frequency and precision for .xtc file nstxtcout = 50 xtc-precision = 1000 -; This selects the subset of atoms for the xtc file. You can +; 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 @@ -68,20 +72,22 @@ energygrps = nstlist = 5 ; ns algorithm (simple or grid) ns_type = grid -; Periodic boundary conditions: xyz (default), no (vacuum) -; or full (infinite systems only) +; Periodic boundary conditions: xyz, no, xy pbc = xyz +periodic_molecules = no ; nblist cut-off rlist = 0.9 -domain-decomposition = no +; long-range cut-off for switched potentials +rlistlong = -1 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Cut-off rcoulomb-switch = 0 rcoulomb = 0.9 -; Dielectric constant (DC) for cut-off or DC of reaction field +; 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 @@ -91,6 +97,8 @@ rvdw = 0.9 DispCorr = EnerPres ; 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 @@ -104,6 +112,9 @@ 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 @@ -112,15 +123,25 @@ 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 - -; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) -implicit_solvent = No +; 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 = berendsen +nsttcouple = -1 +nh-chain-length = 10 ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) @@ -129,13 +150,44 @@ ref_t = 300 ; Pressure coupling Pcoupl = berendsen Pcoupltype = isotropic +nstpcouple = -1 ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 0.5 compressibility = 4.5e-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 = no @@ -156,7 +208,7 @@ constraints = none ; Type of constraint algorithm constraint-algorithm = Lincs ; Do not constrain the start configuration -unconstrained-start = no +continuation = no ; Use successive overrelaxation to reduce the number of shake iterations Shake-SOR = no ; Relative tolerance of shake @@ -177,6 +229,19 @@ morse = no ; 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 @@ -194,21 +259,29 @@ orire = no orire-fc = 0 orire-tau = 0 orire-fitgrp = -; Output frequency for trace(SD) to energy file +; Output frequency for trace(SD) and S to energy file nstorireout = 100 -; Dihedral angle restraints: No, Simple or Ensemble +; Dihedral angle restraints: No or Yes dihre = No dihre-fc = 1000 -dihre-tau = 0 -; Output frequency for dihedral values to energy file -nstdihreout = 100 ; Free energy control stuff free-energy = no init-lambda = 0 delta-lambda = 0 +foreign_lambda = sc-alpha = 0 +sc-power = 0 sc-sigma = 0.3 +nstdhdl = 10 +separate-dhdl-file = yes +dhdl-derivatives = yes +dh_hist_size = 0 +dh_hist_spacing = 0.1 +couple-moltype = +couple-lambda0 = vdw-q +couple-lambda1 = vdw-q +couple-intramol = no ; Non-equilibrium MD stuff acc-grps = @@ -216,6 +289,7 @@ accelerate = freezegrps = freezedim = cos-acceleration = 0 +deform = ; Electric fields ; Format is number of terms (int) and for all terms an amplitude (real)