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

Ah, yes, the fun of force-field building. For the answer to a simple geometry optimization, see I. Camps response below. Skip to the end if you want what is a more general answer to building an entire ...
B. Kelly's user avatar
  • 4,376
10 votes

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

All Gaussian jobs when completed without any error, will have, at the end of the output file, a phrase/thought/quote from someone famous. It is kind off an easteregg. My latest Gaussian successful job ...
Camps's user avatar
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8 votes
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How can I decide on the order of different monomers in a co-polymer?

This is a question that cannot have a "right" answer. As mentioned in the comments, the answer would depend on the experimental system and on the specific properties you want to reproduce. ...
lr1985's user avatar
  • 476
8 votes
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Derivation on correlation function and response functions in polymer physics

It looks Doi makes some extra simplifications (beyond expanding the exponential) that are valid when the external field is weak. Let's start with what you wrote and make one simplification, $$ \begin{...
wcw's user avatar
  • 1,893
8 votes
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What kind of systems do we need to coarse-grain to observe interesting phenomena?

"What kind of systems do we need to coarse-grain to observe interesting phenomena?" Systems that would otherwise be too large and/or complicated to simulate in a reasonable amount of time ...
Nike Dattani - No Free Time's user avatar
7 votes
Accepted

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

This is a very good and tricky question, which I don't think has a clear and definite answer. I think I should also preface by saying that I can't answer it from the point of view of polymer physics, ...
Godzilla's user avatar
  • 1,948
6 votes

Benchmarking Monte Carlo simulations of polymers

Alot of the early pioneering in Monte Carlo (MC) moves were done initially using lattices. While I am not directly aware of places to look for benchmarks, the pioneers in the 90's for Monte Carlo ...
Wesley's user avatar
  • 1,040
6 votes

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

I fear that GROMACS may not be able to capture the interaction you are talking about (If someone is an expert in GROMACS please correct me). This sort of pi-stacking interaction will likely result in ...
Tristan Maxson's user avatar
6 votes
Accepted

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

Doi makes this slightly more confusing because just after these equations, he writes: Here for simplicity we have dropped the subscript q. So all of the pieces of your Eqs \eqref{7} and \eqref{8} ...
Tyberius's user avatar
  • 15.6k
6 votes

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

The answer given by @NikeDattani is very complete. My two cents... As the systems get bigger and bigger and the computational resources, even with the GPU development, doesn't grow in the same speed, ...
Camps's user avatar
  • 23.6k
6 votes

DFT calculation for conjugated polymers

Apologies I do not have enough reputation points to post this as a comment. You might have already considered other electronic structure methods, but I would like to suggest consider using density ...
squareroottwo's user avatar
5 votes
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How to compute the density of the spherical polymer using radius as a bin from the lammps trajectory?

Understanding the Error: Reason you get the error is because you are trying to divide two numpy arrays of unequal shape. len(volumes)=32 len(counts)=33 Therefore, ...
Vandan Revanur's user avatar
5 votes
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gyration radius of short freely jointed chain with excluded volume

When your joints aren't free What's the next thing you see? It's an angle With joints correlated Your chain's free-rotated With an angle $\overline{\cos \theta}$ was once null But now the LJ hull ...
Shern Ren Tee's user avatar
5 votes

Molecular dynamics: how to pack system for desired density

Finally, I just used simulated annealing of NPT ensemble: heated it above glass transition temperature and cooled back down. It equilibrated to the density very close to experimental. Hope my ...
Roman's user avatar
  • 2,373
5 votes
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Derivation of probability density of isolated polymers

For context to future readers, Doi starts with a model of an $N$ unit polymer formed by a random walk along a uniform grid of lattice length $b$. It seems to be implicitly assumed in the described ...
Tyberius's user avatar
  • 15.6k
4 votes

Modelling Diffusion of Molecules Through a Physical Barrier

The challenge of studying diffusion through physical barriers is that these processes can take on the order of microseconds or seconds. Therefore studying the molecular dynamics of a long trajectory, ...
Cody Aldaz's user avatar
  • 8,017
4 votes

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

Based on your previous questions, I assume this equation was from Section 1.2.1 of Doi's Polymer Physics. While Doi doesn't explicitly state this anywhere that I can find, $\mathbf{q}$ is the label he ...
Tyberius's user avatar
  • 15.6k
4 votes

What formula should I use to calculate the total energy of a linear polymer chain?

The difference between total potential energy and total energy is just the kinetic energy, which is the sum of the kinetic energies of your particles, $$E_K = \frac{1}{2}\sum_{i=1}^3 m_i v_i^2$$ where ...
Hayden S's user avatar
  • 940
3 votes
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How should I calculate total potential in a polymer chain?

You'll want to add up all interactions that you can, up to some appropriately chosen cutoff distance. Choose the VDW cutoff such that the total energy doesn't change much if you further increase this ...
Hayden S's user avatar
  • 940
3 votes

Simulating polymers using cellular automata?

Eventually, the question should be more detailed. However, for starters and in general, I would start by giving a cursory read to any wide piece of work that contains this problem, in order to get ...
agaitaarino's user avatar
  • 1,501
3 votes

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

Elastic constants can be calculated using two approach, one with Energy-strain relationship and another with stress-strain relationship. The key ingredient in above two methods is energy or stress at ...
Pranav kumar's user avatar
  • 4,278
2 votes
Accepted

Discrete lattice polymer simulations

Ironically, there exist no on-lattice software for such a Flory-Huggins software. This is primarily because there are no set standards for running such simulations! Most people run their own DIY code ...
megamence's user avatar
  • 4,171
2 votes

How do I calculate the acceptance criterion for configuration bias sampling of my polymer?

From my little experience I would start by defining a spin value for "this site has solvent instead of polymer". (It could replace your existing "no polymer here" spin value, or be ...
Shern Ren Tee's user avatar
2 votes

How to generate a polymer in different conformations?

You could try to run a GROMACS simulation with COLVARS, which takes the radius of gyration as a possible collective variable. Running an umbrella sampling simulation with a suitable set of weights ...
Shern Ren Tee's user avatar
2 votes

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

Regardless of whether you just want to build a 3D structure of PEG20 (which requires only the .gro file), or actually simulate it (which requires both, a .gro file and a topology), I wouldn't start ...
Bdrs's user avatar
  • 271
2 votes

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

I would like to suggest any easy tools for this if you don't want to code. You can use CHARMM Polymer builder for this purpose. In CHARMM Polymer builder, under a single chain, look for Polyethylene ...
Roshan Shrestha's user avatar
1 vote

Complex formation site between polymer and external compound

Actually, the best way to do that is just using normal MD programs like Gromacs to find appropriate sites. If the polymer is not too long, some more accurate methods like xtb from Grimme or even DFT ...
Duy-Minh Hoang's user avatar
1 vote

End-to-end correlation of polymers not decorrelating

The problem with this moveset is that it is too local. The best way to decorrelate polymer configurations is to run simulations with more aggressive moves, such as chain regrowth.
megamence's user avatar
  • 4,171
1 vote

How to check for phase separation in polymer simulations?

Turns out the best way to spot phase transitions in polymers is to run the extended cell simulations and calculate surface tension, as seen in this paper: http://dx.doi.org/10.1063/1.3227905.
megamence's user avatar
  • 4,171
1 vote

Generating topology for charged molecules

There are two options here and the choice depends on what you intend to do with your results. If you are going to perform QM calculations after MD, then you can just alter the charges as you outlined ...
kskinnerx16's user avatar
  • 1,546

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