GROMACS version:2018.8
GROMACS modification: Yes/No
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Here is my code, I want to construct methane gas under certain temperature and pressure conditions by applying pressure to the graphene above, but I am not very clear about how to define the direction of stretching in the pull code. The size of the graphene plate is 5.185nm*4.262 nm, and 1.799 is the force I calculated on graphene at 300 bar. But according to the current situation, it is difficult to achieve a reasonable density of methane. I don’t know which part of my code has the problem, please give me some advice.
; title = constant-force
define =
; Run parameters
integrator = md
dt = 0.001
tinit = 0
nsteps = 500000 ; 500 ps
nstcomm = 500
; Output parameters
nstxout = 500 ; every 1 ps
nstvout = 500
nstfout = 500
nstxout-compressed = 500 ; every 1 ps
nstenergy = 500
;comm-grps = system
; Bond parameters
;constraint_algorithm = lincs
;constraints = h-bonds
;continuation = yes ; continuing from NPT
; Single-range cutoff scheme
cutoff-scheme = Verlet
;ns_type = grid
rcoulomb = 1.55
rvdw = 1.55
; PME electrostatics parameters
coulombtype = PME
; optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl = V-rescale
tc_grps = CH4 fix compr
tau_t = 0.2 0.2 0.2
ref_t = 418 418 418
; Pressure coupling is on
;Pcoupl = Parrinello-Rahman
;pcoupltype = semiisotropic
;tau_p = 5.0
;compressibility = 4.5e-5
;ref_p = 1.0
;refcoord_scaling = com
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr = no
; Pull code
pull = yes
pull-ngroups = 1
pull-group1-name = compr
pull-coord1-type = constant-force
pull-coord1-geometry = direction
pull-coord1-vec = 0 0 -1
pull-coord1-groups = 1 2
pull-coord1-dim = N N Y
pull-coord1-k = -1.799 ; kJ mol^-1 nm^-1
;
freezegrps = compr fix
freezedim = Y Y N Y Y Y
