[gmx-users] micelle formation

[Mark Abraham]

On 17/01/2012 7:37 PM, dina dusti wrote:
> Dear Specialists,
>
> I am a beginner in grmacs and I have several questions about formation 
> of micelle in gromacs. Please help me.
> 1- We know that there is a thermodynamic equilibrium between created 
> micelle and free monomers in solvent, but I don't see this in results 
> of my simulation! When I add the number of monomers, all of them are 
> aggregated depend of concentration of solution in one micelle 
> (spherical to cylindrical) or several micelles and always, lack of 
> single monomer is the most stable state for system. also, I didn't 
> find this in previous work by gromacs.  Is it the limitation of 
> gramacs? Why?

It has nothing to do with GROMACS, and likely everything to do with your 
choice of model physics and the degree of convergence of the simulation.

> 2- What is the relation of radius of gyration with effective radius of 
> spherical micelle that in many of papers have been pointed to 
> R(micelle)=(1.291)R(gyration)?

I don't understand your question, or how it relates to GROMACS :)

> 3- Where is the center of mass of micelle in gromacs, exactly? I 
> obtained rdf for tails of surfactants with center of mass of micelle 
> that the first part of file is as following:( I work with martini and 
> we know that sigma= 0.47 nm in L-J)
>       0                0
>      0.002          0
>      0.004          0
>      0.006          0
>      0.008          0
>       0.01          0
>      0.012          0
>      0.014          0
>      0.016          0
>      0.018          0
>       0.02          0
>      0.022          0
>      0.024          0
>      0.026          0
>      0.028          0
>       0.03          0
>      0.032          0
>      0.034    91.8328
>      0.036          0
>      0.038          0
>       0.04          0
>      0.042    60.1866
>      0.044          0
>      0.046     50.176
>      0.048    46.0824
>       0.05    42.4701
>      0.052    39.2663
>      0.054          0
>      0.056    33.8578
>      0.058          0
>       0.06    29.4943
>      0.062    27.6223
>      0.064          0
>      0.066    48.7518
>      0.068          0
>       0.07    21.6699
>      0.072          0
>      0.074    19.3906
>      0.076          0
>      0.078          0
>       0.08    82.9561
>      0.082    47.3753
>      0.084          0
>      0.086          0
>      0.088          0
>       0.09    39.3277
>      0.092          0
>      0.094    12.0173
>      0.096    23.0438
>      0.098    11.0564
>        0.1          0
>      0.102    20.4125
>      0.104     19.635
>      0.106    9.45052
>      0.108    9.10376
>       0.11    17.5514
>      0.112          0
>      0.114          0
>      0.116    7.89139
> ...............................
> ................................
> ...............................
> What does it mean? Does it say me that the center of micelle is where 
> the end of tails reach together. Do the tails bond in the center of 
> micelle together or there is a hole according to my result and what is 
> your definition in gromacs for center of mass of micelle, hole or bond 
> between tails, Please?

We don't even know whether your micelles should have monomer tails in 
the center or outside, or how you generated those numbers or what they 
are. If that's a radial distribution function, then you probably want to 
choose a narrower bin width for computing it, and get a lot more samples 
to go in it.

> I took rdf for last bead of tails together that the first part of file 
> is as:
>         0          0
>      0.002          0
>      0.004          0
>      0.006          0
>      0.008          0
>      ..............................0
>      ..............................0
>      ..............................0
>      0.414          0
>      0.416          0
>      0.418          0
>       0.42          0
>      0.422          0
>      0.424          0
>      0.426  0.0577916
>      0.428          0
>       0.43   0.113443
> and maximum g(r) is in 0.512 nm (the first peak) and in distance 0.47 
> nm, g(r) is 50.3262. Can I interpret that tails are in two states 
> together: bonded and non-bonded but maximum of tails are non-bonded, 
> therefore, there is a hole in the center of micelle?

I don't know, but some well-chosen use of g_rdf or g_density might get 
the information you seek if it's there to be found. Make sure you 
visualize the simulation first.

Mark
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