Editing TIP4P2005f-N500.mdp


 ;	Created by:
 ;	                     :-) GROMACS - gmx grompp, 2016.4 (-:
 ;	 
 
 ; 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               = md
 ; Start time and timestep in ps
 tinit                    = 0
 dt                       = 0.0002
 nsteps                   = 10000000
 ; 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
 ; group(s) for center of mass motion removal
 comm-grps                = SOL 
 
 ; LANGEVIN DYNAMICS OPTIONS
 ; Friction coefficient (amu/ps) and random seed
 bd-fric                  = 0
 ld_seed                  = 234542354 
 
 ; 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                  = 0
 nstvout                  = 0
 nstfout                  = 0
 ; Output frequency for energies to log file and energy file
 nstlog                   = 10000
 nstcalcenergy            = 100
 nstenergy                = 1000
 ; Output frequency and precision for .xtc file
 nstxout-compressed       = 10000
 compressed-x-precision   = 10000
 ; 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        = 
 ; Selection of energy groups
 energygrps               =  
 
 ; NEIGHBORSEARCHING PARAMETERS
 ; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)
 cutoff-scheme            = Verlet
 ; nblist update frequency
 nstlist                  = 5
 ; ns algorithm (simple or grid)
 ns_type                  = grid
 ; Periodic boundary conditions: xyz, no, xy
 pbc                      = xyz
 periodic_molecules       = no
 ; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,
 ; a value of -1 means: use rlist
 verlet-buffer-tolerance  = 0.005
 ; nblist cut-off        
 rlist                    = 0.8
 ; long-range cut-off for switched potentials
 
 ; OPTIONS FOR ELECTROSTATICS AND VDW
 ; Method for doing electrostatics
 coulombtype              = pme
 coulomb-modifier         = Potential-shift-Verlet
 rcoulomb-switch          = 0
 rcoulomb                 = 0.8
 ; Relative dielectric constant for the medium and the reaction field
 epsilon-r                = 1
 epsilon-rf               = 0
 ; Method for doing Van der Waals
 vdw-type                 = cut-off
 vdw-modifier             = Potential-shift-Verlet
 ; cut-off lengths       
 rvdw-switch              = 0.8
 rvdw                     = 0.8
 ; Apply long range dispersion corrections for Energy and Pressure
 DispCorr                 = EnerPres
 ; 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           = 0.1
 ; FFT grid size, when a value is 0 fourierspacing will be used
 fourier-nx               = 0
 fourier-ny               = 0
 fourier-nz               = 0
 ; EWALD/PME/PPPM parameters
 pme_order                = 4
 ewald-rtol               = 1e-05
 ewald-rtol-lj            = 0.001
 lj-pme-comb-rule         = Geometric
 ewald-geometry           = 3d
 epsilon-surface          = 0
 
 ; IMPLICIT SOLVENT ALGORITHM
 implicit-solvent         = No 
 
 ; GENERALIZED BORN ELECTROSTATICS
 ; Algorithm for calculating Born radii
 gb-algorithm             = Still
 ; Frequency of calculating the Born radii inside rlist
 nstgbradii               = 1
 ; Cutoff for Born radii calculation; the contribution from atoms
 ; between rlist and rgbradii is updated every nstlist steps
 rgbradii                 = 1
 ; Dielectric coefficient of the implicit solvent
 gb-epsilon-solvent       = 80
 ; Salt concentration in M for Generalized Born models
 gb-saltconc              = 0
 ; Scaling factors used in the OBC GB model. Default values are OBC(II)
 gb-obc-alpha             = 1
 gb-obc-beta              = 0.8
 gb-obc-gamma             = 4.85
 gb-dielectric-offset     = 0.009
 sa-algorithm             = Ace-approximation
 ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
 ; The value -1 will set default value for Still/HCT/OBC GB-models.
 sa-surface-tension       = -1 
 
 ; OPTIONS FOR WEAK COUPLING ALGORITHMS
 ; Temperature coupling  
 Tcoupl                   = v-rescale
 nsttcouple               = 1
 nh-chain-length          = 10
 print-nose-hoover-chain-variables = no
 ; Groups to couple separately
 tc-grps                  = SOL
 ; Time constant (ps) and reference temperature (K)
 tau_t                    = 1.3
 ref_t                    = 298
 ; pressure coupling     
 Pcoupl                   = parrinello-rahman
 pcoupltype               = isotropic
 nstpcouple               = 1
 ; Time constant (ps), compressibility (1/bar) and reference P (bar)
 tau_p                    = 2.3
 compressibility          = 4.5e-5
 ref_p                    = 1
 ; Scaling of reference coordinates, No, All or COM
 refcoord-scaling         = No 
 
 ; OPTIONS FOR QMMM calculations
 QMMM                     = no
 ; Groups treated Quantum Mechanically
 QMMM-grps                = 
 ; QM method             
 QMmethod                 = 
 ; QMMM scheme           
 QMMMscheme               = normal
 ; QM basisset           
 QMbasis                  = 
 ; QM charge             
 QMcharge                 = 
 ; QM multiplicity       
 QMmult                   = 
 ; Surface Hopping       
 SH                       = 
 ; CAS space options     
 CASorbitals              = 
 CASelectrons             = 
 SAon                     = 
 SAoff                    = 
 SAsteps                  = 
 ; Scale factor for MM charges
 MMChargeScaleFactor      = 1
 ; Optimization of QM subsystem
 bOPT                     = 
 bTS                      =  
 
 ; SIMULATED ANNEALING   
 ; Type of annealing for each temperature group (no/single/periodic)
 annealing                = no
 ; 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                  = no
 gen_temp                 = 298
 gen_seed                 = -1      
 
 ; OPTIONS FOR BONDS    
 constraints              = none
 ; 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                = 1e-6
 ; Highest order in the expansion of the constraint coupling matrix
 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.
 lincs-iter               = 1
 ; Lincs will write a warning to the stderr if in one step a bond
 ; rotates over more degrees than
 lincs-warnangle          = 30
 ; Convert harmonic bonds to morse potentials
 morse                    = no 
 
 ; ENERGY GROUP EXCLUSIONS
 ; Pairs of energy groups for which all non-bonded interactions are excluded
 energygrp-excl           =   
 
 ; WALLS                
 ; Number of walls, type, atom types, densities and box-z scale factor for Ewald
 nwall                    = 0
 wall-type                = 9-3
 wall-r-linpot            = -1
 wall-atomtype            = 
 wall-density             = 
 wall-ewald-zfac          = 3   
 
 ; COM PULLING          
 pull                     = no  
 
 ; ENFORCED ROTATION     
 ; Enforced rotation: No or Yes
 rotation                 = no   
 
 ; Group to display and/or manipulate in interactive MD session
 IMD-group                =   
 
 ; NMR refinement stuff 
 ; Distance restraints type: No, Simple or Ensemble
 disre                    = No
 ; Force weighting of pairs in one distance restraint: Conservative or Equal
 disre-weighting          = Conservative
 ; Use sqrt of the time averaged times the instantaneous violation
 disre-mixed              = no
 disre-fc                 = 1000
 disre-tau                = 0
 ; Output frequency for pair distances to energy file
 nstdisreout              = 100
 ; Orientation restraints: No or Yes
 orire                    = no
 ; Orientation restraints force constant and tau for time averaging
 orire-fc                 = 0
 orire-tau                = 0
 orire-fitgrp             = 
 ; Output frequency for trace(SD) and S to energy file
 nstorireout              = 100  
 
 ; Free energy variables
 free-energy              = no
 couple-moltype           = 
 couple-lambda0           = vdw-q
 couple-lambda1           = vdw-q
 couple-intramol          = no
 init-lambda              = -1
 init-lambda-state        = -1
 delta-lambda             = 0
 nstdhdl                  = 50
 fep-lambdas              = 
 mass-lambdas             = 
 coul-lambdas             = 
 vdw-lambdas              = 
 bonded-lambdas           = 
 restraint-lambdas        = 
 temperature-lambdas      = 
 calc-lambda-neighbors    = 1
 init-lambda-weights      = 
 dhdl-print-energy        = no
 sc-alpha                 = 0
 sc-power                 = 1
 sc-r-power               = 6
 sc-sigma                 = 0.3
 sc-coul                  = no
 separate-dhdl-file       = yes
 dhdl-derivatives         = yes
 dh_hist_size             = 0
 dh_hist_spacing          = 0.1  
 
 ; Non-equilibrium MD stuff
 acc-grps                 = 
 accelerate               = 
 freezegrps               = 
 freezedim                = 
 cos-acceleration         = 0
 deform                   =  
 
 ; simulated tempering variables
 simulated-tempering      = no
 simulated-tempering-scaling = geometric
 sim-temp-low             = 300
 sim-temp-high            = 300  
 
 ; Electric fields      
 ; Format is number of terms (int) and for all terms an amplitude (real)
 ; and a phase angle (real)
 E-x                      = 
 ; Time dependent (pulsed) electric field. Format is omega, time for pulse
 ; peak, and sigma (width) for pulse. Sigma = 0 removes pulse, leaving
 ; the field to be a cosine function.
 E-xt                     = 
 E-y                      = 
 E-yt                     = 
 E-z                      = 
 E-zt                     =   
 
 ; Ion/water position swapping for computational electrophysiology setups
 ; Swap positions along direction: no, X, Y, Z
 swapcoords               = no
 adress                   = no 
 
 ; User defined thingies
 user1-grps               = 
 user2-grps               = 
 userint1                 = 0
 userint2                 = 0
 userint3                 = 0
 userint4                 = 0
 userreal1                = 0
 userreal2                = 0
 userreal3                = 0
 userreal4                = 0