Merge branch 'v2.2' into v2.3

[makedoc]

user-doc/tutorials/belfast-9a/system/#mdout.mdp.1#

-;
-;	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

user-doc/tutorials/belfast-9a/system/#mdout.mdp.2#

-;
-;	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

user-doc/tutorials/belfast-9a/system/#mdout.mdp.3#

-;
-;	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

user-doc/tutorials/belfast-9a/system/#mdout.mdp.4#

-;
-;	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

user-doc/tutorials/belfast-9a/system/mdout.mdp

 ;
 ;	File 'mdout.mdp' was generated
 ;	By user: carlo (501)
-;	On host: Carlos-MacBook-Pro.local
-;	At date: Thu May 29 23:17:49 2014
+;	On host: Carlos-MBP.fritz.box
+;	At date: Sun Oct 16 17:33:14 2016
 ;
 
 ; VARIOUS PREPROCESSING OPTIONS
@@ -59,16 +59,17 @@ 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
+nstxout-compressed       = 10
+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               = 
 
 ; NEIGHBORSEARCHING PARAMETERS
-; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs)
+; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)
 cutoff-scheme            = Verlet
 ; nblist update frequency
 nstlist                  = 10
@@ -77,9 +78,9 @@ 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,
+; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,
 ; a value of -1 means: use rlist
-verlet-buffer-drift      = 0.0001
+verlet-buffer-tolerance  = 0.0001
 ; nblist cut-off        
 rlist                    = 0.9
 ; long-range cut-off for switched potentials
@@ -116,9 +117,10 @@ 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
-optimize_fft             = yes
 
 ; IMPLICIT SOLVENT ALGORITHM
 implicit_solvent         = No
@@ -221,7 +223,7 @@ 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.
@@ -253,6 +255,9 @@ pull                     = no
 ; 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
@@ -321,12 +326,19 @@ sim-temp-high            = 300
 ; 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 parameters    
 adress                   = no
 

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.