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10 votes

Why are Coulomb interactions modeled with just r, not r squared?

The force $F$ is proportional to $\frac{1}{r^2}$ but the potential $V$ is proportional to $\frac{1}{r}$. This is because $F$ is proportional to $\frac{\partial V}{\partial r}$, the derivative of $V$ ...
Nike Dattani - No Free Time's user avatar
9 votes

How to identify small molecules in a structure without bonds

I used OpenBabel with the --separate option. From the documentation: --separate Separate disconnected fragments into individual ...
Camps's user avatar
  • 23.4k
8 votes

How to choose between Molecular Dynamics and Monte Carlo when beginning to simulate either equilibrium or non-equilibrium systems?

The main difference between MD and MC is, MD is a deterministic method, and MC is a probabilistic method. So, MC is unable to simulate something which needs total accuracy. For instance, if you want ...
user366312's user avatar
  • 2,546
8 votes
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Clustering Algorithms with Periodic Boundary Conditions

First, there is a recent paper in which they proposed a k-means clustering algorithm adapted for periodic boundary conditions. Their Python implementation is available here. However, the clustering ...
Shaun Han's user avatar
  • 1,885
8 votes

Effect of temperature on Forcefield parameters in classical molecular dynamics simulations

The answer to how much information are we losing by considering a temperature-independent forcefield in such systems? is, to a first approximation, none. The reason is that the statement ...
Shern Ren Tee's user avatar
8 votes

Which MD software is preferable for protein simulation?

There is no one size fits all answer here. The best answer depends on exactly what kind of protein simulation you'd like to perform. In particular, a few points to consider: What force field you want ...
Hayden S's user avatar
  • 940
7 votes

Are MD and MC both able to study both equilibrium and non-equilibrium systems?

Monte Carlo methods such as FCIQMC can study non-equilibrium systems: in fact FCIQMC is used for calculating the ground state energy of a system that is already in equilibrium. Monte Carlo methods can ...
Nike Dattani - No Free Time's user avatar
7 votes
Accepted

I was wondering how I should interpret the results of my molecular dynamics simulation

I couldn't completely understand your question, but I will mention some general back-of-the-napkin criteria to be sure that the MD simulation is doing what you think it is doing. These criteria are ...
Mohamed's user avatar
  • 695
7 votes
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Effect of temperature on Forcefield parameters in classical molecular dynamics simulations

I have reasonable experience with the parameterization and MD simulations of molecules with CHARMM FF, which is one of the temperature-agnostic FF. I will try to answer the questions, but please note ...
Hemanth Haridas's user avatar
7 votes
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How do we calculate diffusion coefficient when GROMACS MSD graph with two slopes?

In order to calculate the diffusion coefficient from the MSD plot, you can use this equation: MSD(t) = 6Dt where MSD(t) is ...
Jaafar Mehrez's user avatar
7 votes

How to identify small molecules in a structure without bonds

You ask for either software or algorithm. Other answers speak to existing software. The underlying algorithms generally revolve around interatomic distances. For instance, one chooses a suitable ...
John Bollinger's user avatar
6 votes
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Are MD and MC both parts of statistical physics?

Monte Carlo methods are a broad class of algorithms that apply not just to physics problems but also to biology, finance, and even pure mathematics (for example it can be used to provide better and ...
Nike Dattani - No Free Time's user avatar
6 votes
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Order Parameter for Water in an MD Trajectory: Understanding Changes in Oxygen-Oxygen-Oxygen Triplet Angular Distributions

While there are a number of order parameters which can track the phase transitions and other physio-chemical changes, what you are asking here is about the tetrahedral orientational factor (OTO) which ...
mykd's user avatar
  • 2,342
6 votes
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Speed of atom from kinetic energy of molecule

What is the kinetic energy of a molecule? There is not just one type of kinetic energy when we have a composite system (made up of more than one particle, as in the case of a molecule). For example, ...
Nike Dattani - No Free Time's user avatar
6 votes

Calculation of pH in Molecular Dynamics simulation?

What matters is the number of "free" H+ ions. A quick estimation using the autoionization constant of water shows that the H+ concentration is on the order of $10^{-15}$ mol/L. Obviously, it ...
wzkchem5's user avatar
  • 9,670
6 votes

Are there scripts available for AIMD?

I see you used the the tag 'abinit' so I assume you want to do AIMD with abinit. Abinit's documentation is incredible and you should be able to make a lot of progress by looking there! See e.g. the ...
Tyler Sterling's user avatar
6 votes

Are there scripts available for AIMD?

Just adding to Tyler Sterling's excellent answer, there is also the CASTEP plane-wave DFT program, which is free for academic use (in fact any non-commercial use) and has quite a lot of MD ...
Phil Hasnip's user avatar
  • 7,982
5 votes

How may I create an interatomic potential using DFT?

Developing a potential requires three steps, and then iteration over these steps, as described: (i) Training data Density functional theory (DFT) training data, often in the form of MD NPT simulations,...
Andy Duff's user avatar
5 votes
Accepted

Are MD and MC both able to study both equilibrium and non-equilibrium systems?

Nike's answer included examples of Monte Carlo in the context of electronic structure. However, Monte Carlo techniques are most popularly employed in statistical physics / thermodynamics - often ...
Susi Lehtola's user avatar
  • 19.7k
5 votes
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Classical MD Simulation for mineralization process

Fair Note: I have experience with only studying aggregation of small molecules at the solid - liquid interface. If you are trying to study the formation of an ordered structure from a solution phase ...
Hemanth Haridas's user avatar
5 votes

How may I make a slab surface to calculate a thin layer with Quantum ESPRESSO?

I think that you have probably mistakenly taken Quantum ESPRESSO (QE) as a geometry builder tool. You CANNOT construct thin layers or slab surfaces from bulk using QE. QE is a tool to calculate ...
Abdul Muhaymin -Free Palestine's user avatar
5 votes

How to build up a supercell for explicit solvent system?

1. Using ASE GUI You can utilize ase gui to build supercell manually. Open ASE GUI window with two molecules (for example ase gui emim.xyz bf4.xyz). Then create new ...
mjhong's user avatar
  • 71
5 votes
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Keeping a coarse grained particle off plane (Molecular Dynamics)

It is very difficult to say how you should do what you want ("keep a bead off a plane of other beads") without knowing why you want to do so. So, concretely, let's say I'm modelling a lipid ...
Shern Ren Tee's user avatar
5 votes
Accepted

What is the difference between a "periodic image" and a "nearest image" in MD simulation?

You can generate a periodic image n times in any direction. In comparison, the nearest image is the one that is calculated as +x or -x in the x-direction, +y or -y in the y-direction and +z or -z in ...
Hemanth Haridas's user avatar
5 votes

How to maintain constant liquid density during AIMD with NPT ensembe?

In an AIMD simulation the system size will be very small, so a constant pressure ensemble will entail relatively large volume fluctuations. You should stick to a constant volume simulation unless you ...
Shern Ren Tee's user avatar
5 votes
Accepted

Software for storing information of large number of atomic structures into database file

One of the more recent options for the xyz file format is bqbtool by Martin Brehm, which significantly compresses the trajectory files by factor of 20~30 using a lossless compression scheme. One of ...
mykd's user avatar
  • 2,342
5 votes

Basic MD in ASE

Without further looking into the details, I can tell you straight-up why you cannot get any meaningful result. You are using the EMT calculator, which is a semi-empirical potential parameterized for ...
Shaun Han's user avatar
  • 1,885
5 votes

Is the following description talking about the simulation box or the boundary condition?

It's not talking about either, although it is related to those. They are restraining their system by adding a harmonic potential at the "boundary", which will prevent atoms from escaping. A ...
Phil Hasnip's user avatar
  • 7,982
5 votes
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How is the equation for the position of a virtual site derived?

The formula (1) in the question: $$ \mathbf{r}_s = \underset{\text{term A}}{\mathbf{r}_i} + \underset{\text{term B}}{d \cos\theta\, \frac{\mathbf{r}_{ij}}{|\mathbf{r}_{ij}|}} + \underset{\text{term C}}...
Shern Ren Tee's user avatar
5 votes
Accepted

ASE: Shape mismatch when using FrechetCellFilter filter

I think your NPT object expects a plain Atoms object, and not the Filter object that you get when doing ...
flokno's user avatar
  • 136

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