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

[Justin Lemkul]

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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