;
; 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