[gmx-users] Re,I have a problem with my biphasic system

[Ali Alizadeh]

Dear Justin

Thank you for your reply.

I'm studying hydrate formation, my temprature and pressure are 240 k and
300 bar,

 This is my mdp.file:

title       = OPLS Lysozyme NPT equilibration
define            =     ; position restrain the protein
; Run parameters
integrator  = md        ; leap-frog integrator
nsteps            = 15000000
dt          = 0.002
emtol       = 10.0
emstep          = 0.00001
; Output control
nstxout           = 5000
nstvout           = 5000
nstenergy   = 5000
nstlog            = 5000
nstxtcout       = 5000
xtc_precision   = 5000
; Bond parameters
continuation      = no        ; Restarting after NVT
constraint_algorithm = lincs  ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter  = 1         ; accuracy of LINCS
lincs_order = 4         ; also related to accuracy
; Neighborsearching
ns_type           = grid            ; search neighboring grid cells
nstlist           = 1         ; 10 fs
rlist       = 1.0       ; short-range neighborlist cutoff (in nm)
rcoulomb    = 1.0       ; short-range electrostatic cutoff (in nm)
rvdw        = 1.0       ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME       ; Particle Mesh Ewald for long-range electrostatics
pme_order   = 4         ; cubic interpolation
fourierspacing    = 0.16            ; grid spacing for FFT
ewald_geometry  = 3d
; Temperature coupling is on
tcoupl            = berendsen ; modified Berendsen thermostat
tc-grps           = System    ; two coupling groups - more accurate
tau_t       = 0.1 ; time constant, in ps
ref_t       = 240 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl            = berendsen ; Pressure coupling on in NPT
pcoupltype  = isotropic ; uniform scaling of box vectors
tau_p       = 2.0       ; time constant, in ps
ref_p       = 300.0           ; reference pressure, in bar
compressibility = 4.5e-5      ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc         = xyz       ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel           = no        ; Velocity generation is off




>Ali wrote:
> I have a system that contains water , methane and propane in 240 k and 300
> bar,
>
> My simulation box is rectangular .
>
> Water film is in middle of my box. Methane and propane is around it.
>
> I have a problem, my methane and propane molecules do not diffuse in water
> film(even my methane molecules),
>
> I do simulation, 30 nano second
>
> methane molecules = 834
> propane molecules = 92
> water molecules = 1656
>
> These links is related to md.mdp and .mdp for energy minimization
>
> http://trainbit.com/files/1132999884/md.mdp
> http://trainbit.com/files/2132999884/minim.mdp
>
>
Justin wrote:
The permissions on your files are set such that no one else can view them.

Why would you expect your alkanes to dissolve in water?  The solubility of
methane is very small (roughly 0.02 g/kg of water at 25 C, or about 0.0014
M).
Given this information, in your very small system, basically no methane
molecules would ever partition into the water layer.  I didn't do the
back-of-the-envelope calculations for propane, but you get the idea.

-Justin


-- 
Sincerely

Ali Alizadeh