mdp for membranes

mdps/ff_aa_npt.mdp

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+; 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                       = 0.005
+nsteps                   = _SET_ 
+; 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                  = 20
+; 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                  = -1
+
+; 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                   = 50000
+nstcalcenergy            = 20 
+nstenergy                = 50000
+; Output frequency and precision for .xtc file
+nstxout-compressed       = 50000
+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        = system
+; Selection of energy groups
+energygrps               = system
+
+; NEIGHBORSEARCHING PARAMETERS
+; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)
+cutoff-scheme            = verlet
+; nblist update frequency
+nstlist                  = 20
+; 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  = -1 
+; nblist cut-off        
+rlist                    = _SET_; around 10% more than cut-off 
+; long-range cut-off for switched potentials
+
+; OPTIONS FOR ELECTROSTATICS AND VDW
+; Method for doing electrostatics
+coulombtype              = Cut-off
+coulomb-modifier         = Potential-shift-Verlet
+rcoulomb-switch          = 0
+rcoulomb                 = _SET_
+; 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
+rvdw                     = _SET_ 
+; 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-rtol-lj            = 0.001
+lj-pme-comb-rule         = Geometric
+ewald-geometry           = 3d
+epsilon-surface          = 0
+
+; OPTIONS FOR WEAK COUPLING ALGORITHMS
+; Temperature coupling  
+tcoupl                   = No
+nsttcouple               = 20
+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                    = 25; can be modified to improve diffusion 
+ref_t                    = _TEMP_ 
+; pressure coupling     
+Pcoupl                   = c-rescale
+pcoupltype               = semiisotropic
+nstpcouple               = -1
+; Time constant (ps), compressibility (1/bar) and reference P (bar)
+tau-p                    = 50
+compressibility          = 4.5e-5  4.5e-5 
+ref-p                    = 1. 1.
+; Scaling of reference coordinates, No, All or COM
+refcoord-scaling         = No
+
+; GENERATE VELOCITIES FOR STARTUP RUN
+gen_vel                  = no
+gen_temp                 = _TEMP_ 
+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                = 0.0001
+; 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               = 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
+