Questions tagged [polymers]
Questions related to polymers.
38
questions
15
votes
2
answers
800
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(...
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14
votes
1
answer
115
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 ...
- 1,407
12
votes
2
answers
434
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 ...
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12
votes
1
answer
169
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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 ...
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11
votes
1
answer
154
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
1
answer
203
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 ...
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9
votes
1
answer
172
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 ...
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9
votes
1
answer
511
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 ...
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9
votes
1
answer
738
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, ...
- 191
9
votes
1
answer
97
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 ...
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8
votes
1
answer
100
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 ...
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7
votes
1
answer
282
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 ...
- 2,363
7
votes
0
answers
162
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 ...
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6
votes
1
answer
58
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 ...
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6
votes
1
answer
86
views
End-to-end correlation of polymers not decorrelating
I am running Monte Carlo simulations of polymers with nearest neighbor interactions only. For benchmarking purposes, I decided to run some excluded volume simulations (no overlaps) allowed on a 3D ...
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6
votes
1
answer
108
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 ...
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6
votes
0
answers
45
views
How to rigorously prove the existence of a coil-globule transition of polymers in an on-lattice simulation? [closed]
I am running on-lattice simulations of polymers. I am testing out different Hamiltonians and testing different regimes to test if they yield interesting behavior. My question is, how do I rigorously ...
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6
votes
0
answers
125
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%...
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5
votes
1
answer
128
views
DFT calculation for conjugated polymers
I am new to DFT calculation.
I want to know the structure of conjugated polymers (plane angle, etc.) and their electronic and optical properties (such as HOMO-LUMO, IR, etc.).
I am using 6-311+G(d) ...
5
votes
1
answer
121
views
gyration radius of short freely jointed chain with excluded volume
The freely jointed chain model without excluded volume has the following gyration radius,
$$
\langle R_g^2 \rangle=\frac{1}{6}\frac{N+2}{N+1}Na^2
$$
where $N$ is the number of bonds and $a$ their ...
5
votes
1
answer
81
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 $\mathbf{R}$, ...
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5
votes
0
answers
42
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 ...
- 51
4
votes
1
answer
182
views
How to compute the density of the spherical polymer using radius as a bin from the lammps trajectory?
I am working on condensate studies and I did form a globular condensate of the polymer system using lammps. I wanted to find out the number density of condensate with respect to the radius as bins to ...
- 43
4
votes
1
answer
95
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 ...
- 57
4
votes
1
answer
116
views
How to generate a polymer in different conformations?
I want to run MD simulations of a polymer, but I want to start from different physical conformations. My question is, how do I obtain these conformations? Is there a software which performs this?
Let'...
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4
votes
1
answer
61
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-...
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4
votes
0
answers
71
views
Statistical properties of semi-flexible polymers
I am reading Statistical Physics of Particles by Kardar. I am struggling with problem 12d, in chapter 2, about semi-flexible polymers in two dimensions. The problem is as follows:
Configurations of a ...
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4
votes
0
answers
61
views
Where should I apply the harmonic spring function in the case of polymer simulation? [closed]
I need to simulate the off-lattice movement of a polymer chain in a 3D space using Monte Carlo simulation. Note this is not a simulation of polymer growth; rather this is about polymer movement/motion....
- 2,352
4
votes
0
answers
68
views
What does it mean by pruning and enrichment in the case of Rosenbluth method? [closed]
As far as I understand:
Pruning means deleting something.
Enrich means to enhance/increase weight.
Now my question is, in the case of pruned-enriched Rosenbluth method (PERM):
For pruning/enriching, ...
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3
votes
1
answer
69
views
What formula should I use to calculate the total energy of a linear polymer chain?
I am using the Bead-spring model to model a polymer chain.
Suppose, the polymer has 3 monomers in its chain:
$$\ce{A1-A2-A3}$$
And,
I can use the following formula to calculate the total Lennard-Jones ...
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3
votes
1
answer
57
views
How should I calculate total potential in a polymer chain?
Suppose, a polymer has 3 monomers in its chain:
$$\ce{A1-A2-A3}$$
When calculating total LJ potential, do I need to calculate like this:
$$E(r_{12})+E(r_{23})+E(r_{31})$$
Or, do I calculate: $$E(r_{12}...
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3
votes
1
answer
28
views
How do I calculate the acceptance criterion for configuration bias sampling of my polymer?
I am running a lattice simulation of a single chain polymer on a lattice with every other site occupied by solvent. The additional wrinkle is that every particle on the lattice has a number/spin ...
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3
votes
0
answers
58
views
What is the efficiency of Nylon/Polyethylene artificial muscles? [closed]
The only other question in regards to this subject doesn't have a precise answer and it is more about actuators that directly convert electricity into mechanical force.
Nylon or polyethylene fibers, ...
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3
votes
0
answers
130
views
Molecular MC simulation is not equilibrating [closed]
Suppose, a polymer has N monomers in its chain. I want to simulate its movement using the bead-spring model.
So, I wrote the following program in Python.
Polymer chain simulation with Monte Carlo ...
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2
votes
0
answers
58
views
Simulate liquid solvent mobility through a gel polymer electrolyte
I would like to simulate a liquid solvent (such as TEGDME) embedded into a polymeric cage (such as PEGDM). What is the most meaningful approach to estimate transport properties in such a system?
Three ...
- 667
1
vote
0
answers
16
views
Complex formation site between polymer and external compound
I am studying about conjugated polymers in sensors applications. I want to conduct structural of complex and its properties (such as HOMO-LUMO etc.). Is there any software for docking that external ...
1
vote
0
answers
72
views
Temperature damping parameter in lammps [closed]
I need help on how to set Tdamping in MD simulation. In Lammps documentation it is mentioned that the typical value is 100 for nvt, but when I put this value to my ...
- 11
1
vote
0
answers
61
views
Polymer simulation [closed]
I am absolutely new to Polymer simulation. I am trying to understand the simulation by analyzing source code written by others.
Can anyone tell me what are the differences between the following three ...
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