;
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0
;
; for use with GROMACS 3.3
;

; VARIOUS PREPROCESSING OPTIONS = 
title                    = Martini
cpp                      = /usr/bin/cpp

; RUN CONTROL PARAMETERS = 
; MARTINI - Most simulations are stable with dt=40 fs,
; some (especially rings) require 20-30 fs.
; The range of time steps used for parametrization  
; is 20-40 fs, using smaller time steps is therefore not recommended.

integrator               = md
; start time and timestep in ps
tinit                    = 0.0
dt                       = 0.02
nsteps                   = 36000000 ; gives simulation time of 720 ns or 0.72 us
; number of steps for center of mass motion removal 
nstcomm                  = 1
comm-grps		 = 

; OUTPUT CONTROL OPTIONS = 
; Output frequency for coords (x), velocities (v) and forces (f) = 
nstxout                  = 0 ; default 5000
nstvout                  = 0 ; default 5000
nstfout                  = 0
; Output frequency for energies to log file and energy file = 
nstlog                   = 10000
nstenergy                = 10000
; Output frequency and precision for xtc file = 
nstxtcout                = 10000 ; default 1000
xtc_precision            = 100
; This selects the subset of atoms for the xtc file. You can = 
; select multiple groups. By default all atoms will be written. = 
xtc-grps                 = 
; Selection of energy groups = 
energygrps               = 

; NEIGHBORSEARCHING PARAMETERS = 
; MARTINI - no need for more frequent updates 
; or larger neighborlist cut-off due
; to the use of shifted potential energy functions.

; nblist update frequency = 
nstlist                  = 10
; ns algorithm (simple or grid) = 
ns_type                  = grid
; Periodic boundary conditions: xyz or none = 
pbc                      = xyz
; nblist cut-off         = 
rlist                    = 1.2

; OPTIONS FOR ELECTROSTATICS AND VDW = 
; MARTINI - vdw and electrostatic interactions are used
; in their shifted forms. Changing to other types of
; electrostatics will affect the general performance of
; the model.

; Method for doing electrostatics = 
coulombtype              = Shift 
rcoulomb_switch          = 0.0
rcoulomb                 = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field = 
epsilon_r                = 15
; Method for doing Van der Waals = 
vdw_type                 = Shift 
; cut-off lengths        = 
rvdw_switch              = 0.9
rvdw                     = 1.2
; Apply long range dispersion corrections for Energy and Pressure = 
DispCorr                 = No

; OPTIONS FOR WEAK COUPLING ALGORITHMS = 
; MARTINI - normal temperature and pressure coupling schemes 
; can be used. It is recommended to couple individual groups
; in your system seperately.

; Temperature coupling   = 
tcoupl                   = Berendsen
; Groups to couple separately = 
tc-grps                  = DPPC DUPC CHOL W
; Time constant (ps) and reference temperature (K) = 
tau_t                    = 0.3 0.3 0.3 0.3
ref_t                    = 290 290 290 290
; Pressure coupling      = 
Pcoupl                   = berendsen 
Pcoupltype               = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) = 
tau_p                    = 3.0 3.0
compressibility          = 3e-5 3e-5
ref_p                    = 1.0 1.0

; GENERATE VELOCITIES FOR STARTUP RUN = 
gen_vel                  = no
gen_temp                 = 323
gen_seed                 = 666

; OPTIONS FOR BONDS     = 
; MARTINI - for ring systems constraints are defined
; which are best handled using Lincs. 

constraints              = none 
; Type of constraint algorithm = 
constraint_algorithm     = Lincs
; Do not constrain the start configuration = 
unconstrained_start      = no
; Highest order in the expansion of the constraint coupling matrix = 
lincs_order              = 4
; Lincs will write a warning to the stderr if in one step a bond = 
; rotates over more degrees than = 
lincs_warnangle          = 30

4004