; ; 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. integrator = md dt = 0.03 nsteps = 50000 nstcomm = 100 comm-grps = nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstenergy = 100 nstxout-compressed = 1000 compressed-x-precision = 100 compressed-x-grps = energygrps = DPPC W ; 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 = 15 ; 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 = DPPC W tau_t = 1.0 1.0 ref_t = 320 320 Pcoupl = parrinello-rahman Pcoupltype = semiisotropic tau_p = 12.0 ;parrinello-rahman is more stable with larger tau-p, DdJ, 20130422 compressibility = 3e-4 3e-4 ref_p = 1.0 1.0 gen_vel = no gen_temp = 320 gen_seed = 473529 ; MARTINI and CONSTRAINTS ; for ring systems and stiff bonds constraints are defined ; which are best handled using Lincs. constraints = none constraint_algorithm = Lincs