coarse-grained crosslink structure/define bead in polymer solution/calculation of Flory-Huggins parameter
Dear All I'm trying to simulate the condensation of CH3Si(OH)4 which derived from methyltrimethoxysilane(MTMS) hydrolysis. Thanks to Jason's crosslink script, the crosslink simulation can be completed. Words can't express how grateful I am for his help. Really appreciate that. Actually what I need to do is not only crosslink simulation, but also DPD simulation. By the way, in my supervisor's group, I am the first postgraduate student to study molecular simulation, so I can't get help from people around me. Everything in this community is so helpful. Thank you all. There are a few questions I face when I want to do DPD simulation. The system is about poly( CH3Si(OH)4) and water as solvent. Q1. When defining the beads, I think there should be two types of beads(A and B) which represent polymer and water respectively. And the relative molecular mass one bead contains should be equal approximately. Is my thought right? Q2. Type A bead contains polymer, and I assume that there should be several monomers which has already be crosslinked completely in the bead. I've read an article about the definition way of a similar system and that author contained four monomers in one DPD bead, so it is a 4-ring. (Multiscale molecular simulation of nanostructured systems, Chapter 5.3.2,Paola Posocco ) Q3.The most important thing in DPD simulation is the calculation about Flory-Huggins parameter so as to getaij. And there are several equations about it.
(1) (2) (3) aij = 25+3.27Xij
Now here are the steps I assume that might be taken to calculate Chi parameter(please tell me what is the right way): First, I should construct enough amout(maybe 100?) of monomers in a AC box in liquid density and complete the crosslink simulation. Then, run Forcite "cohesive energy density" to get (Ecoh/V). Sprt it and we can get solubility paremeter of polymer. Second, run simulation to get solubility paremeter of solvent(water). Third, in equation(1), if the "RT" changes to "kT", "V" is the molar volume of solution? Forth, define beads, calculate aij.
And above is my thought. I'm sure I have many mistakes. Please point it out and teach me how to do it correctly. Thank you all.
Yes, traditionally beads are defined with equal mass. Hence if one bead respresents a CH₃Si(OH)₃ molecule, it corresponds to about 5 water molecules. Assuming 30 Å³ per water molecule, such bead has a volume of 150 Å³ or 90 cm³/mole beads.
To obtain the repsulsion parameter, run a NPT simulation of pure CH₃Si(OH)₃ and again for pure water. Calculate the solubility parameters Eq. (2) using the trajectories. Then Eq. (1) will predict the χ-parameter, where ν is the molar bead volume, i.e. 90 cm³/mol. Finally Eq. (3) provides the repulsion parameter. This should provide a reasonable estimate for the interaction in the network environment too. Note Eq. (3) assumes a density of 3 beads per unit volume.
Hi Reinier Thank you so much for your explanations. So kind of you! And your words match well with my ideas about the steps I should do, and really encourage me a lot. But I think there is still a big question remaining unsolved. How to define the polymer bead? You know, this polymer has crosslinking structure which is totally different with copolymer or homopolymer, so there is no repeat unit actually. So I was wondering, if , we could sketch a 4-ring(maybe 5 or 6, any number suitable) polymer and define it as a bead(A). Then we define another type B bead, which has equal mass as A ,about H2O .
I am not in this research area any more, so I rarely check my MS community account. And I hope you have already solved this problem yourself, cause it has been 10days since your reply and it was an easy problem. I'am so sorry if your research is impeded only because of my late reply.
I store all my MS files in another hard disk which is not on my hand, so I dont have the file now. But I can tell you how to build the input xsd file.
Step1: Set up an empty xsd file, let me call it 01.xsd. and build one CH3Si(OH)3 moelcular in 01.xsd.
Step2: use the Amorphous Cell module to set up a box which contains 100CH3Si(OH)3 (maybe 1000, if you like), you must set 01.xsd as the original file.
These two steps are very easy. I assume that you are a new learner of MS. I suggest, you can get help from your surrouding senior fellows. That will be more effective that asking people online.
if you still have any questions, just post it here and I will reply as soon as possible.