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?
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)?
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?
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?
Please help me.
Thank you very much in advance.
Best Regards
Dina
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