A little background: I am an undergraduate student, a biochemistry major with little to no background in bioinformatics. We're only allowed to choose dry lab topics for our thesis since we cannot go to school to perform experiments in the chem lab.
I am currently very, very lost regarding on what to do with my thesis entitled: PHASE DIAGRAM FOR PHASE SEPARATION OF POLY(METHYL METHACRYLATE) COPOLYMERS USING FIELD-THEORETIC SIMULATION. I have been following works by Mr. Fredrickson and colleagues but they are difficult for me to understand.
My progress so far is that I've ran the Gromacs input files I've made in CHARMM Polymer Builder in SLURM HPC (these input files vary in solvents so that I could investigate the effect of addition of solvent to the phase separation). Now, as you can read in my title, I have to construct phase diagrams. Any help on how to construct phase diagrams (through FTS)? Thank you so much!
As far as I understand, you are going a wrong way. MD simulations of polymers cannot give you any phase-diagram, and they are very computationally expensive.
You refer to field theoretic approach of Fredrickson and others, which is essentially a mean field approach, where you reach equilibrium density distributions of molecular species in a self-consistent manner. Consequently, there is no molecular dynamics and you work with coarse-grained beads that represent the whole monomer instead of real atoms.
You may start with a bit of polymer physics, mean field approaches, and Flory-Huggins theory. The method is called the self-consistent field theory, which is essentially a classical density functional theory. I think you may have to write your own program for simulations. You may read one of my old papers, and the references there in.
Article Self‐Consistent Field Modeling of Three‐Dimensional Morpholo...
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