12 votes
Accepted

Why do the peaks in a radial distribution function graph have a probability >1

The radial distribution function isn't a probability or a probability density. The usual definition is $$g(r)=\frac{\rho(r)}{\rho_0}$$ where $\rho(r)$ is the number density at a particular distance $r$...
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  • 11.3k
9 votes
Accepted

Why aren't the Anton computers used more widely?

Protein dynamics occur in multiple different time scales. I myself is a person using MD simulation for my research. One reason I am not so much interested in ANTON is not it's cost, limited resource ...
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7 votes

Boltzmann Distribution in Molecular Dynamics Simulation?

Within statistical mechanics (SM) a molecular property $X$ is computed by $$\left<{X}\right>_{SM}=\sum^{states}_i X_i p_i$$where $X_i$ is the value of $X$ for energy state $i$ and $p_i$ is the ...
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  • 4,759
7 votes
Accepted

Hessian Matrix and Physical directions: Potential Energy Surface

I think you have the causality backwards here. It's not as if we have the vibrations to start with and they happen to be matched by the eigenvectors of the Hessian. We choose to look at these ...
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7 votes
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SARS-CoV - relative size of the spike protein

Although this is a homework question, I also think OP deserves a help as orthocresol suggested. I'm not going to go into details but leave it at orthocresol's suggestion of this being a Western Blot ...
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5 votes

Calculate force on atoms given the energy of configuration, trajectory of simulation and position of atoms in each frame

tl,dr: Forces are equivalent to the negative of the gradient, use small, arbitrary $\mathrm{d}r$ for each atom The problem, as you mention, with many neural network methods in chemistry at the moment,...
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5 votes
Accepted

Is it true that an evaporating molecule has the same kinetic energy as a molecule in a pot of boiling water?

Is it true that an evaporating molecule has the same kinetic energy as a molecule in a pot of boiling water? Well for one the kinetic energy for a given temperature is an average kinetic energy of a ...
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  • 11.9k
5 votes
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How to perform molecular dynamics simulations of charged systems?

This is intrinsic to Ewald summation methods, not software implementations. The uniform charge arises from neglect of a reciprocal sum term. It does not directly affect the dynamics and may be a ...
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  • 271
5 votes

Why aren't the Anton computers used more widely?

Anton and its successor Anton2 are highly specialized pieces of machinery. In fact, the computer, the chip, and the only code that can run on the chip are all called Anton. There's a reason why the ...
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  • 1,500
5 votes

How much time for a water molecule in pure water to reach the top of a glass of water?

I am posting here the answer since it has been quickly found thanks to the useful comments. To give an estimate the best way is to look at the self-diffusion coefficient. This is defined as the ...
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  • 1,616
5 votes
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Practical use of the partition function in molecular simulations

The actual partition function is unimaginably formidable. For just $N$ point particles in a 3D box, it's already got $3N$ dimensions. If the box is length $L$, GROMACS would probably divide the box ...
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4 votes

Boltzmann Distribution in Molecular Dynamics Simulation?

This question is actually very broad as the answer can change quite a bit based on what kind of thing you are doing with your MD simulation. The first thing to note is that the Boltzmann distribution ...
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4 votes
Accepted

How to write an entire trajectory into a single PDB file?

...
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4 votes

Why are MD (Molecular Dynamics) simulations performed at room temperature for the purposes of studying proteins?

Another reason why people don't bother to use 310K versus 300K is because any time you are using MD, you have an approximate force field describing the dynamics of the system which means you have an ...
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4 votes

What causes energy peaks during a molecular dynamics energy minimization?

At the top of your config file, you imply that you want to perform an NVE calculation, but you’re actually doing NVT, because you have the Langevin thermostat turned on. Langevin works by giving the ...
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3 votes

Is there a known relation between the diffusion of a molecule and the diffusion of the reactants?

More a set of queries and comments than an answer. I don't understand why you make A and B vary with time irrespective of your reaction scheme. You should really analyse using Fick's diffusion ...
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3 votes

How did Noe et al. derive $k_{AB}$ in their PNAS 2009 paper?

Let us start by defining all the terms in Eq. 1 carefully, as the OP does not do so. I have always found it easier to interpret such models in the context of particles flowing from state to state, and ...
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3 votes

Is it true that an evaporating molecule has the same kinetic energy as a molecule in a pot of boiling water?

Seems true just by the definition of boiling point. At boiling point your liquid is in equilibrium between its liquid and gas phases, hence the "average" molecule will possess that minimum amount of ...
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  • 1,462
3 votes

Why are MD (Molecular Dynamics) simulations performed at room temperature for the purposes of studying proteins?

This depends on the organism you are studying. I work with Bac and human, I have simulations running at 300k and 310k. Search on the organism you are going to work on and adjust its temperament for ...
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3 votes
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Fixing incongruities in PES Scan

Even without seeing your molecule, I can say the referee is very likely correct. If you think of doing a scan of the dihedral of hydrogen peroxide, by symmetry the path from $\theta=180\to360$ should ...
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3 votes
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Would there be need for periodic DFT if we are able to get all the forcefields of all the elements in the periodic table in ReaxFF?

Quoting from the article The ReaxFF reactive force-field: development, applications and future directions "Such empirical methods, including reactive force-field (ReaxFF),1 trade accuracy for lower ...
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  • 2,463
3 votes

Vibrational state dependency of the reaction cross section

Vibrations are very important for reactions. In the particular example of $\ce{H2+(g) + He}$ vibrational levels 0-3 have an energy less than E0 (minimum energy for reaction), so additional ...
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3 votes
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Calculation of free energy from potential and kinetic energy

The sum of the potential and kinetic energies is the internal energy, E (or U). However, you don't necessarily need to know the entropy to calculate the free energy. If you perform an equilibrium ...
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  • 11.6k
2 votes
Accepted

What types of energies can be determined by molecular dynamics in gas phase or explicit solvents?

First, whether you use DFT or molecular mechanics to get your energies and forces doesn't really matter. If you have equations of motion, forces, and energies then you have the dynamics necessary to ...
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  • 12.6k
2 votes

Why are MD (Molecular Dynamics) simulations performed at room temperature for the purposes of studying proteins?

You want to be able to compare your simulation with the real world, and that means you do (or look at other's) in vitro experiments, which are predominantly (at least for starters) done at room ...
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  • 11.4k
2 votes

Difference between Force Field and topology, and other related questions

1 - "Force Field" (FF) means the set of equations that describe the interactions between atoms and the set of numerical parameters that people using those particular functions have come up with to ...
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