diff --git a/user-doc/tutorials/belfast-9a/system/#mdout.mdp.1# b/user-doc/tutorials/belfast-9a/system/#mdout.mdp.1# deleted file mode 100644 index 0bcacab74147bd0b40e6623f64525b426997a4bf..0000000000000000000000000000000000000000 --- a/user-doc/tutorials/belfast-9a/system/#mdout.mdp.1# +++ /dev/null @@ -1,343 +0,0 @@ -; -; File 'mdout.mdp' was generated -; By user: carlo (501) -; On host: Carlos-MacBook-Pro.local -; At date: Thu May 29 00:44:02 2014 -; - -; VARIOUS PREPROCESSING OPTIONS -; 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 -integrator = sd -; Start time and timestep in ps -tinit = 0 -dt = 0.002 -nsteps = 1000 -; 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 = 10 -; 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 = 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 = 10000 -nstvout = 10000 -nstfout = 0 -; Output frequency for energies to log file and energy file -nstlog = 10000 -nstcalcenergy = -1 -nstenergy = 1000 -; Output frequency and precision for .xtc file -nstxtcout = 10 -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 = protein -; Selection of energy groups -energygrps = - -; NEIGHBORSEARCHING PARAMETERS -; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs) -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 drift due to the Verlet buffer in kJ/mol/ps per atom, -; a value of -1 means: use rlist -verlet-buffer-drift = 0.0001 -; nblist cut-off -rlist = 0.9 -; long-range cut-off for switched potentials -rlistlong = -1 -nstcalclr = -1 - -; OPTIONS FOR ELECTROSTATICS AND VDW -; Method for doing electrostatics -coulombtype = pme -coulomb-modifier = Potential-shift-Verlet -rcoulomb-switch = 0 -rcoulomb = 0.9 -; 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 -vdw-modifier = Potential-shift-Verlet -; cut-off lengths -rvdw-switch = 0 -rvdw = 0.9 -; 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_geometry = 3d -epsilon_surface = 0 -optimize_fft = yes - -; 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 = 2.092 - -; OPTIONS FOR WEAK COUPLING ALGORITHMS -; Temperature coupling -tcoupl = No -nsttcouple = -1 -nh-chain-length = 10 -print-nose-hoover-chain-variables = no -; Groups to couple separately -tc-grps = system -; Time constant (ps) and reference temperature (K) -tau_t = 1 -ref_t = 278 -; pressure coupling -Pcoupl = No -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 - -; 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 = 278.0 -gen_seed = -1 - -; 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 = 2 -; 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 - -; ENFORCED ROTATION -; Enforced rotation: No or Yes -rotation = 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 - -; Free energy variables -free-energy = no -couple-moltype = -couple-lambda0 = vdw-q -couple-lambda1 = vdw-q -couple-intramol = no -init-lambda = 0 -init-lambda-state = -1 -delta-lambda = 0 -nstdhdl = 10 -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 = 0 -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 = -E-xt = -E-y = -E-yt = -E-z = -E-zt = - -; AdResS parameters -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 diff --git a/user-doc/tutorials/belfast-9a/system/#mdout.mdp.2# b/user-doc/tutorials/belfast-9a/system/#mdout.mdp.2# deleted file mode 100644 index c09776c10a4d5232cb57217c318ec8fc507d03bf..0000000000000000000000000000000000000000 --- a/user-doc/tutorials/belfast-9a/system/#mdout.mdp.2# +++ /dev/null @@ -1,343 +0,0 @@ -; -; File 'mdout.mdp' was generated -; By user: carlo (501) -; On host: Carlos-MacBook-Pro.local -; At date: Thu May 29 23:17:46 2014 -; - -; VARIOUS PREPROCESSING OPTIONS -; 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 -integrator = sd -; Start time and timestep in ps -tinit = 0 -dt = 0.002 -nsteps = 1000 -; 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 = 10 -; 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 = 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 = 10000 -nstvout = 10000 -nstfout = 0 -; Output frequency for energies to log file and energy file -nstlog = 10000 -nstcalcenergy = -1 -nstenergy = 1000 -; Output frequency and precision for .xtc file -nstxtcout = 10 -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 = protein -; Selection of energy groups -energygrps = - -; NEIGHBORSEARCHING PARAMETERS -; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs) -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 drift due to the Verlet buffer in kJ/mol/ps per atom, -; a value of -1 means: use rlist -verlet-buffer-drift = 0.0001 -; nblist cut-off -rlist = 0.9 -; long-range cut-off for switched potentials -rlistlong = -1 -nstcalclr = -1 - -; OPTIONS FOR ELECTROSTATICS AND VDW -; Method for doing electrostatics -coulombtype = pme -coulomb-modifier = Potential-shift-Verlet -rcoulomb-switch = 0 -rcoulomb = 0.9 -; 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 -vdw-modifier = Potential-shift-Verlet -; cut-off lengths -rvdw-switch = 0 -rvdw = 0.9 -; 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_geometry = 3d -epsilon_surface = 0 -optimize_fft = yes - -; 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 = 2.092 - -; OPTIONS FOR WEAK COUPLING ALGORITHMS -; Temperature coupling -tcoupl = No -nsttcouple = -1 -nh-chain-length = 10 -print-nose-hoover-chain-variables = no -; Groups to couple separately -tc-grps = system -; Time constant (ps) and reference temperature (K) -tau_t = 1 -ref_t = 278 -; pressure coupling -Pcoupl = No -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 - -; 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 = 278.0 -gen_seed = -1 - -; 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 = 2 -; 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 - -; ENFORCED ROTATION -; Enforced rotation: No or Yes -rotation = 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 - -; Free energy variables -free-energy = no -couple-moltype = -couple-lambda0 = vdw-q -couple-lambda1 = vdw-q -couple-intramol = no -init-lambda = 0 -init-lambda-state = -1 -delta-lambda = 0 -nstdhdl = 10 -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 = 0 -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 = -E-xt = -E-y = -E-yt = -E-z = -E-zt = - -; AdResS parameters -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 diff --git a/user-doc/tutorials/belfast-9a/system/#mdout.mdp.3# b/user-doc/tutorials/belfast-9a/system/#mdout.mdp.3# deleted file mode 100644 index 36bc5460591fc48e2038618c6036a90837fcf02b..0000000000000000000000000000000000000000 --- a/user-doc/tutorials/belfast-9a/system/#mdout.mdp.3# +++ /dev/null @@ -1,343 +0,0 @@ -; -; File 'mdout.mdp' was generated -; By user: carlo (501) -; On host: Carlos-MacBook-Pro.local -; At date: Thu May 29 23:17:47 2014 -; - -; VARIOUS PREPROCESSING OPTIONS -; 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 -integrator = sd -; Start time and timestep in ps -tinit = 0 -dt = 0.002 -nsteps = 1000 -; 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 = 10 -; 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 = 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 = 10000 -nstvout = 10000 -nstfout = 0 -; Output frequency for energies to log file and energy file -nstlog = 10000 -nstcalcenergy = -1 -nstenergy = 1000 -; Output frequency and precision for .xtc file -nstxtcout = 10 -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 = protein -; Selection of energy groups -energygrps = - -; NEIGHBORSEARCHING PARAMETERS -; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs) -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 drift due to the Verlet buffer in kJ/mol/ps per atom, -; a value of -1 means: use rlist -verlet-buffer-drift = 0.0001 -; nblist cut-off -rlist = 0.9 -; long-range cut-off for switched potentials -rlistlong = -1 -nstcalclr = -1 - -; OPTIONS FOR ELECTROSTATICS AND VDW -; Method for doing electrostatics -coulombtype = pme -coulomb-modifier = Potential-shift-Verlet -rcoulomb-switch = 0 -rcoulomb = 0.9 -; 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 -vdw-modifier = Potential-shift-Verlet -; cut-off lengths -rvdw-switch = 0 -rvdw = 0.9 -; 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_geometry = 3d -epsilon_surface = 0 -optimize_fft = yes - -; 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 = 2.092 - -; OPTIONS FOR WEAK COUPLING ALGORITHMS -; Temperature coupling -tcoupl = No -nsttcouple = -1 -nh-chain-length = 10 -print-nose-hoover-chain-variables = no -; Groups to couple separately -tc-grps = system -; Time constant (ps) and reference temperature (K) -tau_t = 1 -ref_t = 278 -; pressure coupling -Pcoupl = No -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 - -; 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 = 278.0 -gen_seed = -1 - -; 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 = 2 -; 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 - -; ENFORCED ROTATION -; Enforced rotation: No or Yes -rotation = 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 - -; Free energy variables -free-energy = no -couple-moltype = -couple-lambda0 = vdw-q -couple-lambda1 = vdw-q -couple-intramol = no -init-lambda = 0 -init-lambda-state = -1 -delta-lambda = 0 -nstdhdl = 10 -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 = 0 -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 = -E-xt = -E-y = -E-yt = -E-z = -E-zt = - -; AdResS parameters -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 diff --git a/user-doc/tutorials/belfast-9a/system/#mdout.mdp.4# b/user-doc/tutorials/belfast-9a/system/#mdout.mdp.4# deleted file mode 100644 index a26a8485d54798114c30ac0dfbe3e3ff573a6f92..0000000000000000000000000000000000000000 --- a/user-doc/tutorials/belfast-9a/system/#mdout.mdp.4# +++ /dev/null @@ -1,343 +0,0 @@ -; -; File 'mdout.mdp' was generated -; By user: carlo (501) -; On host: Carlos-MacBook-Pro.local -; At date: Thu May 29 23:17:48 2014 -; - -; VARIOUS PREPROCESSING OPTIONS -; 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 -integrator = sd -; Start time and timestep in ps -tinit = 0 -dt = 0.002 -nsteps = 1000 -; 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 = 10 -; 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 = 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 = 10000 -nstvout = 10000 -nstfout = 0 -; Output frequency for energies to log file and energy file -nstlog = 10000 -nstcalcenergy = -1 -nstenergy = 1000 -; Output frequency and precision for .xtc file -nstxtcout = 10 -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 = protein -; Selection of energy groups -energygrps = - -; NEIGHBORSEARCHING PARAMETERS -; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs) -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 drift due to the Verlet buffer in kJ/mol/ps per atom, -; a value of -1 means: use rlist -verlet-buffer-drift = 0.0001 -; nblist cut-off -rlist = 0.9 -; long-range cut-off for switched potentials -rlistlong = -1 -nstcalclr = -1 - -; OPTIONS FOR ELECTROSTATICS AND VDW -; Method for doing electrostatics -coulombtype = pme -coulomb-modifier = Potential-shift-Verlet -rcoulomb-switch = 0 -rcoulomb = 0.9 -; 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 -vdw-modifier = Potential-shift-Verlet -; cut-off lengths -rvdw-switch = 0 -rvdw = 0.9 -; 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_geometry = 3d -epsilon_surface = 0 -optimize_fft = yes - -; 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 = 2.092 - -; OPTIONS FOR WEAK COUPLING ALGORITHMS -; Temperature coupling -tcoupl = No -nsttcouple = -1 -nh-chain-length = 10 -print-nose-hoover-chain-variables = no -; Groups to couple separately -tc-grps = system -; Time constant (ps) and reference temperature (K) -tau_t = 1 -ref_t = 278 -; pressure coupling -Pcoupl = No -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 - -; 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 = 278.0 -gen_seed = -1 - -; 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 = 2 -; 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 - -; ENFORCED ROTATION -; Enforced rotation: No or Yes -rotation = 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 - -; Free energy variables -free-energy = no -couple-moltype = -couple-lambda0 = vdw-q -couple-lambda1 = vdw-q -couple-intramol = no -init-lambda = 0 -init-lambda-state = -1 -delta-lambda = 0 -nstdhdl = 10 -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 = 0 -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 = -E-xt = -E-y = -E-yt = -E-z = -E-zt = - -; AdResS parameters -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 diff --git a/user-doc/tutorials/belfast-9a/system/#topol.tpr.1# b/user-doc/tutorials/belfast-9a/system/#topol.tpr.1# deleted file mode 100644 index 041a882226a41d78d2fdf81cf9a7e5b66e4cd112..0000000000000000000000000000000000000000 Binary files a/user-doc/tutorials/belfast-9a/system/#topol.tpr.1# and /dev/null differ diff --git a/user-doc/tutorials/belfast-9a/system/nvt.mdp b/user-doc/tutorials/belfast-9a/system/nvt.mdp index 8a27d287dea34e1e1c712afb8bb4fe76fd331a04..af7fdfb90f58cc7a44dd64ff09b1c7945a1a92e5 100644 --- a/user-doc/tutorials/belfast-9a/system/nvt.mdp +++ b/user-doc/tutorials/belfast-9a/system/nvt.mdp @@ -221,7 +221,7 @@ Shake-SOR = no ; Relative tolerance of shake shake-tol = 0.0001 ; Highest order in the expansion of the constraint coupling matrix -lincs-order = 4 +lincs-order = 6 ; 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.