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Questions tagged [polymers]

Questions related to polymers.

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15 votes
2 answers
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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(...
Kavya Mrudula's user avatar
14 votes
1 answer
121 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 ...
Kavya Mrudula's user avatar
12 votes
2 answers
473 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 ...
megamence's user avatar
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12 votes
1 answer
191 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 ...
megamence's user avatar
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12 votes
1 answer
166 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, ...
Jonathon Vandezande's user avatar
10 votes
1 answer
237 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 ...
megamence's user avatar
  • 4,171
9 votes
1 answer
188 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 ...
megamence's user avatar
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9 votes
1 answer
614 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 ...
Kavya Mrudula's user avatar
9 votes
1 answer
809 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, ...
Irina's user avatar
  • 191
9 votes
1 answer
120 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 ...
Kavya Mrudula's user avatar
8 votes
1 answer
109 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 ...
megamence's user avatar
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7 votes
1 answer
373 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 ...
Roman's user avatar
  • 2,373
7 votes
0 answers
177 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 ...
Kavya Mrudula's user avatar
6 votes
1 answer
68 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 ...
megamence's user avatar
  • 4,171
6 votes
1 answer
95 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 ...
megamence's user avatar
  • 4,171
6 votes
1 answer
126 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 ...
megamence's user avatar
  • 4,171
6 votes
0 answers
47 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 ...
megamence's user avatar
  • 4,171
6 votes
0 answers
136 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%...
Irina's user avatar
  • 191
5 votes
1 answer
183 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) ...
Duy-Minh Hoang's user avatar
5 votes
1 answer
139 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 ...
Marco Mendívil Carboni's user avatar
5 votes
1 answer
84 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 $\mathbf{R}$, ...
megamence's user avatar
  • 4,171
5 votes
0 answers
45 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 ...
arun_kol's user avatar
4 votes
1 answer
217 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 ...
kesavan's user avatar
  • 43
4 votes
2 answers
103 views

Given a .gro file of a monomer, how to polymerize it?

I have a structure (.gro) file of a PolyEthylene Glycol (PEG) molecule as shown below. How do I get the corresponding structure file for PEG-20 i.e., a molecule with a degree of polymerization=20, ...
Pranoy Ray's user avatar
  • 1,637
4 votes
1 answer
99 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 ...
omar karbal's user avatar
4 votes
1 answer
126 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'...
megamence's user avatar
  • 4,171
4 votes
1 answer
64 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-...
megamence's user avatar
  • 4,171
4 votes
0 answers
119 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 ...
megamence's user avatar
  • 4,171
4 votes
0 answers
62 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....
user366312's user avatar
  • 2,556
4 votes
0 answers
76 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, ...
user366312's user avatar
  • 2,556
3 votes
1 answer
80 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 ...
user366312's user avatar
  • 2,556
3 votes
1 answer
63 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}...
user366312's user avatar
  • 2,556
3 votes
1 answer
32 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 ...
megamence's user avatar
  • 4,171
3 votes
0 answers
12 views

Diblock building in Biovia material studio

I am trying to build polystyrene and polyethylenepropylene diblock chains. When I assign head and tail and build diblock chain I could see that the atom numbers get flipped, meaning that head and tail ...
Princy David's user avatar
3 votes
0 answers
62 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, ...
Fulano's user avatar
  • 151
3 votes
0 answers
131 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 ...
user366312's user avatar
  • 2,556
2 votes
0 answers
51 views

How do I validate and benchmark a new protein or polymer model?

Suppose I designed a novel coarse-grained model of polymer chains. How can I test the validity of my novel model? Is there any applied framework available?
user366312's user avatar
  • 2,556
2 votes
0 answers
63 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 ...
Marco Di Gennaro's user avatar
1 vote
1 answer
31 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 ...
Duy-Minh Hoang's user avatar
1 vote
0 answers
147 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 ...
Fryad Sharif's user avatar
1 vote
0 answers
73 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 ...
user366312's user avatar
  • 2,556