<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div id="yiv671780235"><div><div style="color:#000;background-color:#fff;font-family:times new roman, new york, times, serif;font-size:12pt;"><div id="yiv671780235yui_3_2_0_16_132678534862140">Dear Specialists,<span><br></span></div><div id="yiv671780235yui_3_2_0_16_132678534862188"><br id="yiv671780235yui_3_2_0_16_1326785348621779"></div><div id="yiv671780235yui_3_2_0_16_132678534862189">I am a beginner in grmacs and I have several questions about formation of micelle in gromacs. Please help me.</div><div id="yiv671780235yui_3_2_0_16_132678534862198">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?<br></div><div id="yiv671780235yui_3_2_0_16_1326785348621332">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)?</div><div id="yiv671780235yui_3_2_0_16_1326785348621525">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)<br></div><div id="yiv671780235yui_3_2_0_16_1326785348621606"> 0 0<br>
0.002 0<br> 0.004 0<br> 0.006 0<br>
0.008 0<br> 0.01 0<br> 0.012 0<br> 0.014 0<br> 0.016 0<br> 0.018 0<br> 0.02 0<br> 0.022 0<br> 0.024 0<br> 0.026 0<br>
0.028 0<br> 0.03 0<br> 0.032 0<br> 0.034 91.8328<br> 0.036 0<br> 0.038 0<br> 0.04 0<br> 0.042 60.1866<br> 0.044 0<br> 0.046 50.176<br> 0.048 46.0824<br> 0.05 42.4701<br>
0.052 39.2663<br> 0.054 0<br> 0.056 33.8578<br> 0.058 0<br> 0.06 29.4943<br> 0.062 27.6223<br> 0.064 0<br> 0.066 48.7518<br> 0.068 0<br> 0.07 21.6699<br> 0.072 0<br> 0.074 19.3906<br> 0.076
0<br> 0.078 0<br> 0.08 82.9561<br> 0.082 47.3753<br> 0.084 0<br> 0.086 0<br> 0.088 0<br> 0.09 39.3277<br> 0.092 0<br> 0.094 12.0173<br> 0.096 23.0438<br> 0.098 11.0564<br> 0.1 0<br>
0.102 20.4125<br> 0.104 19.635<br> 0.106 9.45052<br> 0.108 9.10376<br> 0.11 17.5514<br> 0.112 0<br> 0.114 0<br> 0.116 7.89139</div><div id="yiv671780235yui_3_2_0_16_1326785348621729">...............................<br></div><div id="yiv671780235yui_3_2_0_16_1326785348621730">................................<br></div><div id="yiv671780235yui_3_2_0_16_1326785348621731">...............................<br></div><div id="yiv671780235yui_3_2_0_16_1326785348621732">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? <br></div><div id="yiv671780235yui_3_2_0_16_13267853486211492">I took rdf for last bead of tails together that the first part of file is as:</div> 0 0<br> 0.002 0<br> 0.004 0<br> 0.006 0<br> 0.008 0<br> ..............................0<br> ..............................0<br> ..............................0<br>
0.414 0<br> 0.416 0<br> 0.418 0<br> 0.42 0<br> 0.422 0<br> 0.424 0<br> 0.426 0.0577916<br> 0.428 0<br> 0.43 0.113443<br>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?<br><br>Please help me.<br>Thank you very much in advance.<br><br>Best Regards<br>Dina<br><br><br><br><br> <br><br><br><br><br><br><br></div></div></div></div></body></html>