13_eq50_10fs.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.

title                    = Martini

; 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.

;#define -DPOSRES

integrator               = md
define                   = -DPOSRES -DPOSRES_FC=50
dt                       = 0.01
nsteps                   = 1000000
nstcomm                  = 100

nstxout                  = 0
nstvout                  = 0
nstfout                  = 0
nstlog                   = 1000
nstenergy                = 1000
nstxout-compressed       = 1000
compressed-x-precision   = 100
compressed-x-grps        = 

; 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                  = 20
ns_type                  = grid
pbc                      = xyz
verlet-buffer-tolerance  = 0.005

coulombtype              = reaction-field 
rcoulomb                 = 1.1
epsilon_r                = 2.5 ;  (with polarizable water)
epsilon_rf               = 0
vdw_type                 = cutoff  
vdw-modifier             = Potential-shift-verlet
rvdw                     = 1.1

; 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                   = v-rescale 
tc-grps                  = Protein lipids PW_ION
tau_t                    = 1.0 1.0 1.0 
ref_t                    = 310 310 310

pcoupl                   = Berendsen
pcoupltype               = semiisotropic
tau_p                    = 5 
compressibility          = 3e-4 3e-4 3e-4
ref_p                    = 1.0 1.0 1.0
refcoord-scaling         = all


gen_vel                  = yes
gen_temp                 = 310
gen_seed                 =  -1

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

constraints              = none 
constraint_algorithm     = Lincs
;lincs-iter               = 8
;lincs-order              = 8