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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