Questions tagged [polymers]

Questions related to polymers.

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15
votes
2answers
347 views

What are the parameters that need to be calculated to design the structure of a molecule?

Before performing Molecular Dynamics on a co-polymer that doesn't have a ready-to-use structure anywhere, the monomer fragment was built in Avogadro software with 0 net charge, B3LYP theory and 6-31G(...
14
votes
1answer
95 views

How can I decide on the order of different monomers in a co-polymer?

While performing molecular dynamics simulations on a co-polymer, how long should the minimum size of the polymer be, to replicate the experimental properties with a reasonable error? Within this ...
13
votes
2answers
391 views

What kind of systems do we need to coarse-grain to observe interesting phenomena?

When I go to talks, I hear the statement "coarse-graining is required to access spatio-temporal scales to observe important dynamical behavior for stimuli-responsive systems" before they go ...
11
votes
1answer
109 views

Modelling Diffusion of Molecules Through a Physical Barrier

I would like to model the diffusion of various small molecules (e.g. $\ce{O2}$, $\ce{H2O}$, $\ce{MeOH}$, etc.) through polymeric barrier material (e.g. polyethylene, ethylene vinyl alcohol, ...
10
votes
1answer
133 views

What is the physical meaning of the q in Fourier transforms of correlation functions?

While studying polymer dynamics, one comes across a wide range of correlation functions. A lot of times, we are interested in the Fourier transforms of these functions, as the FT allows us to solve ...
9
votes
1answer
130 views

Derivation on correlation function and response functions in polymer physics

I am reading Introduction to Polymer Physics by Doi and I am having trouble understanding a derivation by him on the concentration fluctuations in polymer solutions. I have outlined his method and ...
9
votes
1answer
148 views

Is there a way to understand pi-pi interactions through GROMACS?

I have two polymer molecules with benzene rings as a part of them. I would like to understand how the interactions between them influences the solvability of the polymer in a non-aqeous solvent. I ...
9
votes
1answer
259 views

Why VASP calculates the elastic constant for another trigonal space group?

Please, help me to understand the problem. I calculated the elastic constants for the beta PHB (Space group P3221 (154)), it has to show the reduced elastic constant matrix (six), however, ...
9
votes
1answer
61 views

Generating topology for charged molecules

I have to generate a topology file for a molecule like Sodium Triphosphate, and I do not find forcefields available in the literature. So as a starting point would like to use engines like LigParGen ...
8
votes
1answer
83 views

How often does one have to run polymer Monte Carlo moves to effectively sample phase space?

I have a polymer and solvent on a lattice, and I am performing an NVT Monte Carlo simulation. I am performing the following moves on it: My question is, how should these moves be conducted to ...
8
votes
0answers
44 views

Benchmarking Monte Carlo simulations of polymers

I have written a simulation engine in C++ to run a Monte Carlo simulation of polymers on a lattice. My code basically plants a polymer on a lattice, and performs certain Monte Carlo moves, including ...
7
votes
0answers
90 views

How to effectively simulate high density systems in GROMACS? [closed]

I have a system with a dense liquid solvent and a polymer solute. I have inserted all the molecules randomly using gmx insert-molecules and then did the energy ...
6
votes
1answer
46 views

Solving for the deviation in the polymer volume fraction under the random phase approximation

I am reading through Introduction to Polymer Physics by Doi, and I am studying the concentration fluctuation in polymer solutions, specifically the random phase approximation. For the most part, I ...
6
votes
1answer
85 views

Molecular dynamics: how to pack system for desired density

I'm trying to perform ab-initio MD on polymer system. I've built single chain of polycarbonate (PC) with the length of ~40 angstroms and now I'm building initial configuration. I've calculated how ...
6
votes
0answers
84 views

How to optimize the geometry of beta PHB in VASP? [closed]

I would like to calculate the elastic constants of beta PHB. From this paper. I know that it has P3221 space group. The beta PHB has upward and downward chains, which exist at one lattice site with 50%...
5
votes
1answer
69 views

Derivation of probability density of isolated polymers

(Crossposted on physics SE) I am reading Introduction to Polymer Physics by Doi, and in his proof for the probability distribution for ideal polymers of length $N$ and end-to-end vector $\mathbf{R}$, ...
5
votes
0answers
37 views

How do I model drug diffusion from polymeric matrix? [closed]

I have been redirected to this forum from Chemistry SE. My problem consists of a structure (say a cylinder) made from a homogenous distribution of a drug from a polymeric matrix. These compounds are ...
4
votes
1answer
77 views

Simulating polymers using cellular automata?

I am a physics student, and I am working on my final year project, I am planning to simulate polymers using cellular automata. I am really struggling with this project, if someone can give me any ...
4
votes
0answers
16 views

How to check for phase separation in polymer simulations?

Suppose I am running a molecular dynamics simulation of a polymer solution that exhibits upper critical solution temperature. From standard solution thermodynamics, we expect to see a polymer-rich ...
4
votes
0answers
28 views

Discrete lattice polymer simulations

I am trying to develop phase coexistence curves for generic polymers. Of course, I can use standard Flory theory free energy functionals to do this, but I want to define my nearest neighbor polymer-...