md_cg.mdp

; STANDARD MD INPUT OPTIONS FOR MARTINI 2.x
; Updated 15 Jul 2015 by DdJ
;
; for use with GROMACS 5
; For a thorough comparison of different mdp options in combination with the Martini force field, see:
; D.H. de Jong et al., Martini straight: boosting performance using a shorter cutoff and GPUs, submitted.

; TIMESTEP IN MARTINI 
; Most simulations are numerically stable with dt=40 fs, 
; however better energy conservation is achieved using a 
; 20-30 fs timestep. 
; Time steps smaller than 20 fs are not required unless specifically stated in the itp file.
integrator               = md
dt                       = 0.009
nsteps                   = 22222222
nstcomm                  = 100

;nstxout                  = 500 
;nstvout                  = 2000
;nstfout                  = 2000
;nstlog                   = 10  
nstenergy                = 2000
nstxout-compressed       = 500 
;compressed-x-precision   = 1000

; NEIGHBOURLIST and MARTINI 
; To achieve faster simulations in combination with the Verlet-neighborlist
; scheme, Martini can be simulated with a straight cutoff. In order to 
; do so, the cutoff distance is reduced 1.1 nm. 
; Neighborlist length should be optimized depending on your hardware setup:
; updating ever 20 steps should be fine for classic systems, while updating
; every 30-40 steps might be better for GPU based systems.
; The Verlet neighborlist scheme will automatically choose a proper neighborlist
; length, based on a energy drift tolerance.
;
; Coulomb interactions can alternatively be treated using a reaction-field,
; giving slightly better properties.
; Please realize that electrostVatic interactions in the Martini model are 
; not considered to be very accurate to begin with, especially as the 
; screening in the system is set to be uniform across the system with 
; a screening constant of 15. When using PME, please make sure your 
; system properties are still reasonable.
;
; With the polarizable water model, the relative electrostatic screening 
; (epsilon_r) should have a value of 2.5, representative of a low-dielectric
; apolar solvent. The polarizable water itself will perform the explicit screening
; in aqueous environment. In this case, the use of PME is more realistic.


cutoff-scheme            = Verlet
nstlist                  = 30
ns_type                  = grid
pbc                      = xyz
verlet-buffer-tolerance  = 0.005

coulombtype              = PME 
coulomb-modifier         = Potential-shift-verlet
rcoulomb                 = 1.2
epsilon_r                = 15  
vdw_type                 = cutoff  
vdw-modifier             = Force-switch         
rvdw                     = 1.2
rvdw-switch		 = 1.0
rlist			 = 1.2

; MARTINI and TEMPERATURE/PRESSURE
; normal temperature and pressure coupling schemes can be used. 
; It is recommended to couple individual groups in your system separately.
; Good temperature control can be achieved with the velocity rescale (V-rescale)
; thermostat using a coupling constant of the order of 1 ps. Even better 
; temperature control can be achieved by reducing the temperature coupling 
; constant to 0.1 ps, although with such tight coupling (approaching 
; the time step) one can no longer speak of a weak-coupling scheme.
; We therefore recommend a coupling time constant of at least 0.5 ps.
; The Berendsen thermostat is less suited since it does not give
; a well described thermodynamic ensemble.
; 
; Pressure can be controlled with the Parrinello-Rahman barostat, 
; with a coupling constant in the range 4-8 ps and typical compressibility 
; in the order of 10e-4 - 10e-5 bar-1. Note that, for equilibration purposes, 
; the Berendsen barostat probably gives better results, as the Parrinello-
; Rahman is prone to oscillating behaviour. For bilayer systems the pressure 
; coupling should be done semiisotropic.

tcoupl                   = Nose-Hoover
tau_t                    = 24.0
ref_t                    = 300 
tc-grps                  = System
Pcoupl                   = parrinello-rahman 
Pcoupltype               = isotropic
tau_p                    = 24.0   ;parrinello-rahman is more stable with larger tau-p, DdJ, 20130422
compressibility          = 4.5e-5
ref_p                    = 1.0  
continuation 		 = no 
gen_vel                  = yes
gen_temp                 = 300

; MARTINI and CONSTRAINTS 
; for ring systems and stiff bonds constraints are defined
; which are best handled using Lincs. 

lincs-iter		 = 2
constraints              = all-bonds  
constraint_algorithm     = lincs 
lincs-order 		 = 16