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

[Justin Lemkul]

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
>
>

-- 
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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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