14

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 force-field. Read the whole thing if you want some insight into force-fields, particularly partial charges. First, doing an electronic structure calculation (...


10

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 finished with this quote: THERE IS NO SCIENCE WITHOUT FANCY, NOR ART WITHOUT FACTS. -- VLADIMIR NABAKOV Anyway, answering your second question: What ...


9

"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 and/or with a reasonable amount of computational resources. Basically if you want to see $t$ seconds of dynamics for $N$ atoms, and your computational-resources/...


8

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{eqnarray} \overline{\delta \phi _a} &= \frac{\langle\delta \phi_a \rangle -\langle \delta \phi _a \beta U_{ext}\rangle}{\langle 1-\beta U_{ext}\rangle} \tag{...


7

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. Since most experimental systems are in what is known as the "scaling regime" you probably need long polymers to begin with (I commented on the issue ...


7

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, we need to use some approximations if we want to get some knowledge of the system behavior. It is very common to think that molecular dynamics is only used in ...


7

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, but instead from my experience in biomolecular simulations. However, this particular problem is basically a version of the sampling exploration-exploitation ...


6

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 either a charge transfer (if asymmetric) or some sort of pi-pi bonding interaction that a forcefield is unlikely to capture. If you took a snapshot of the MD ...


6

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} are actually the Fourier transforms of the pieces of your \eqref{1} and \eqref{2}, so they should all have q subscripts. Its also common to write Fourier ...


5

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 derivation that the lattice used is $b\mathbb{Z}^3$, that is the uniform 3D grid. Note there are other types of lattices for which Eq.$\,(\ref{2})$ is not true. ...


4

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 uses for the momentum/wavevector. I'm more accustomed to seeing this denoted as $\mathbf{k}$, but as Anyon noted in the comments, $\mathbf{q}$ may be the more ...


4

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 experience will help someone. UPD: Equilibrating the system at very high pressure (I used 1000 bar) also work fine in difficult cases.


4

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, for example to calculate the Free Energy or potential of mean force (PMF) is practically impossible. Nevertheless, a technique which is very promising for ...


3

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 some perspective. For example in the PhD thesis Cellular automata methods in mathematical physics, where chapter 5 is dedicated to Modeling Polymers with Cellular ...


3

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 particular mode of distortion. For example in cubic crystal which have 3 fold symmetry about body diagonal need three independent elastic parameters to define ...


1

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 in your question. This is because QM will correct any issues you might come across. However, you need to make sure the molecule will behave in the manner in ...


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