17
votes
Accepted
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 ...
- 4,266
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 ...
- 20.7k
8
votes
Accepted
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.
...
- 466
8
votes
Accepted
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{...
- 1,863
8
votes
Accepted
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 ...
- 30.8k
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, ...
- 1,878
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 ...
- 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 ...
- 10.6k
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} ...
- 14.5k
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, ...
- 20.7k
5
votes
Accepted
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
...
- 1,016
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 ...
- 2,333
5
votes
Accepted
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 ...
- 14.5k
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, ...
- 7,869
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 ...
- 14.5k
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 ...
- 760
3
votes
Accepted
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 ...
- 760
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 ...
- 1,421
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 ...
- 3,834
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 ...
- 4,091
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 ...
- 1,016
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 ...
- 1,016
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.
- 4,091
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.
- 4,091
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 ...
- 1,526
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