I am trying to run equilibration i gromacs 5.0.7 Implicit solvent. My input file is:

; MD CONTROL OPTIONS

integrator = md

dt = 0.002

nsteps = 50000 ; 10 ns

init_step = 0 ; For exact run continuation or redoing part of a run

comm-mode = Angular ; mode for center of mass motion removal

nstcomm = 10 ; number of steps for center of mass motion removal

; OUTPUT CONTROL OPTIONS

; Output frequency for coords (x), velocities (v) and forces (f)

nstxout = 1000

nstvout = 1000

nstfout = 1000

; Output frequency for energies to log file and energy file

nstlog = 1000

nstcalcenergy = 10

nstenergy = 1000

; Neighbor searching and Electrostatitcs

vdwtype = cut-off

coulombtype = cut-off

;cutoff-scheme = group

pbc = no

periodic_molecules = no

nstlist = 5

ns_type = grid

rlist = 1.0

rcoulomb = 1.6

rvdw = 1.6

; Selection of energy groups

energygrps = fixed not_fixed

freezegrps = fixed not_fixed

freezedim = Y Y Y N N N

;Relative dielectric constant for the medium and the reaction field

epsilon_r = 1

epsilon_rf = 1

; Temperutare coupling

tcoupl = v-rescale

tc_grps = fixed not_fixed

tau_t = 0.01 0.01

;nst_couple = 5

ref_t = 300.00 300.00

; Pressure coupling

pcoupl = no

;pcoupletype = isotropic

tau_p = 1.0

;compressiblity = 4.5e-5

ref_p = 1.0

gen_vel = yes

gen_temp = 300.00 300.00

gen_seed = -1

constraints = h-bonds

; Implicit solvent

implicit_solvent = GBSA

gb_algorithm = Still ; HCT ; OBC

nstgbradii = 1.0

rgbradii = 1.0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist

gb_epsilon_solvent = 80 ; Dielectric constant for the implicit solvent

gb_saltconc = 0 ; Salt concentration for implicit solvent models, currently not used

sa_algorithm = Ace-approximation

sa_surface_tension = 2.05016 ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA. The value -1 will set default value for Still/HCT/OBC GB-models.

However after running

grompp

I am getting errors:

NOTE 1 [file eq_input.mdp, line 72]:

eq_input.mdp did not specify a value for the .mdp option "cutoff-scheme".

Probably it was first intended for use with GROMACS before 4.6. In 4.6,

the Verlet scheme was introduced, but the group scheme was still the

default. The default is now the Verlet scheme, so you will observe

different behaviour.

ERROR 1 [file eq_input.mdp]:

With Verlet lists only full pbc or pbc=xy with walls is supported

ERROR 2 [file eq_input.mdp]:

Implicit solvent is not (yet) supported with the with Verlet lists.

NOTE 2 [file eq_input.mdp]:

With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note

that with the Verlet scheme, nstlist has no effect on the accuracy of

your simulation.

ERROR 3 [file eq_input.mdp]:

The box volume is required for calculating rlist from the energy drift

with verlet-buffer-tolerance > 0. You are using at least one unbounded

dimension, so no volume can be computed. Either use a finite box, or set

rlist yourself together with verlet-buffer-tolerance = -1.

ERROR 4 [file eq_input.mdp]:

With GBSA implicit solvent, rgbradii must be equal to rlist.

What should I use insted of Verlet list? AMy suggestions?