On 11/2/12 6:46 AM, Ali Alizadeh wrote:
Dear Justin
Thank you for reply;
I'm reproducing this paper that related to this topic,
dx.doi.org/10.1088/0953-4075/42/3/035302
It's title : A molecular dynamic study of water/methane/propane
I only had time to quickly look at this paper, but it is clear to me that the
authors do not necessarily report methane partitioning into water from the
external layers, rather their starting configuration has methane embedded in the
water layer to begin with. Their simulations lasted for 105 ns in the ternary
system, though their data analysis of partial densities only includes data up to
40 ns, which I find a bit curious.
-Justin
Sincerely
Ali Alizadeh
On 11/2/12 3:25 AM, Ali Alizadeh wrote:
Dear Justin
Thank you for your reply.
I'm studying hydrate formation, my temprature and pressure are 240 k and
300 bar,
Has anyone ever demonstrated that you can observe such phenomena in an MD
simulation under these conditions?
Also note that you're making your simulations unnecessarily slow using
nstlist =
1, which is only for EM. For MD, a value of 5 or 10 should suffice.
-Justin
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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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