; ; STANDARD MD INPUT OPTIONS FOR MARTINI 2.P (polarizable water model) ; ; for use with GROMACS 4.x ; title = Martini cpp = /usr/bin/cpp ; TIMESTEP IN MARTINI ; Most simulations are numerically stable ; with dt=40 fs, some (especially rings) require 20-30 fs. ; Note that time steps of 40 fs and larger may create local heating or ; cooling in your system. Although the use of a heat bath will globally ; remove this effect, it is advised to check consistency of ; your results for somewhat smaller time steps in the range 20-30 fs. ; Time steps exceeding 40 fs should not be used; time steps smaller ; than 20 fs are also not required. integrator = md tinit = 0.0 dt = 0.02 nsteps = 50000 nstcomm = 1 comm-grps = nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 1000 nstenergy = 100 nstxtcout = 1000 xtc_precision = 100 xtc-grps = energygrps = DPPC PW ; NEIGHBOURLIST and MARTINI ; Due to the use of shifted potentials, the noise generated ; from particles leaving/entering the neighbour list is not so large, ; even when large time steps are being used. In practice, once every ; ten steps works fine with a neighborlist cutoff that is equal to the ; non-bonded cutoff (1.2 nm). However, to improve energy conservation ; or to avoid local heating/cooling, you may increase the update frequency (e.g. nstlist = 5) ; and/or enlarge the neighbourlist cut-off (rlist = 1.4 or 1.5 nm). The latter option ; is computationally less expensive and leads to improved energy conservation nstlist = 10 ns_type = grid pbc = xyz rlist = 1.2 ; MARTINI and NONBONDED ; Standard cut-off schemes are used for the non-bonded interactions ; in the Martini model: LJ interactions are shifted to zero in the ; range 0.9-1.2 nm, and electrostatic interactions in the range 0.0-1.2 nm. ; The treatment of the non-bonded cut-offs is considered to be part of ; the force field parameterization, so we recommend not to touch these ; values as they will alter the overall balance of the force field. ; In principle you can include long range electrostatics through the use ; of PME, which could be more realistic in certain applications ; ; 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. coulombtype = Shift ; PME can also be used with the polariable model rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r = 2.5 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 DispCorr = No ; MARTINI and TEMPRATURE/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 Berendsen thermostat, ; using a coupling constant of the order of τ = 1 ps. Even better ; temperature control can be achieved by reducing the temperature coupling ; constant to 0.1 ps, although with such tight coupling (τ 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. ; ; Similarly, pressure can be controlled with the Berendsen barostat, ; with a coupling constant in the range 1-5 ps and typical compressibility ; in the order of 10-4 - 10-5 bar-1. Note that, in order to estimate ; compressibilities from CG simulations, you should use Parrinello-Rahman ; type coupling. tcoupl = Berendsen tc-grps = DPPC PW tau_t = 1.0 1.0 ref_t = 320 320 Pcoupl = berendsen Pcoupltype = semiisotropic tau_p = 1.0 1.0 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 constraints are defined ; which are best handled using Lincs. ; Note, during energy minimization the constrainst should be ; replaced by stiff bonds. constraints = none constraint_algorithm = Lincs unconstrained_start = no lincs_order = 4 lincs_warnangle = 30