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4 votes

Explain ab initio molecular dynamics like I'm five

As you suspected, molecular dynamics (MD) is simply propagating Newton's II equation of motion ${\bf F}_i = m_i {\bf a}_i$ for the nuclei with masses $m_i$ at positions ${\bf r}_i$, velocities ${\bf v}...
Susi Lehtola's user avatar
  • 19.7k
4 votes
Accepted

Energies from single points vs. AIMD for training Machine Learning Force Fields

In the shortest way possible, temperature cannot be defined for single-point calculations. This is because temperature arises from the kinetic energies of the atoms or ions (nuclei), and a single-...
Andrey Poletayev's user avatar
4 votes

Check for steric clashes before doing minimization

Using Tcl scripting in VMD noh and exwithin 0.5 of noh exwithin is basically the within ...
Vasista's user avatar
  • 1,341
4 votes
Accepted

Check for steric clashes before doing minimization

MolProbity That programs use the Clashscore to account for the number of pairs of atoms in the model that are unusually close to each other. It is expressed as the number or such clashes per thousand ...
Camps's user avatar
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2 votes

Forcefield parameterization techniques

There are many FFs that are available at your disposal, such as CHARMM, AMBER and OPLS. These FFs will have residues that form the part of the protein that you are interested in, and can be directly ...
Hemanth Haridas's user avatar
2 votes

How to reproduce 2D small-angle X-ray scattering (SAXS) interferogram of water via ab-initio MD methods?

In short, there is nothing wrong with the spike that you have obtained. The low-wavevector spike is a general feature of small-angle diffraction. For example, see Figure 1 of this paper where the ...
Andrey Poletayev's user avatar
1 vote
Accepted

How to calculate height of the center of the H2 molecule from surface via ASE?

Here is simple template which print Z-distance between centre of $\ce{H_2}$ molecule and nearest $\ce{Pt}$ atom. Feel free to edit and plot. ...
Pranav kumar's user avatar
  • 4,268
1 vote

LAMMPS structure rotation

It looks like you just need to center the system before the rotation. If you do this, it should line up correctly. ASE may also be a good resource for this type of system manipulation if you dont ...
Tristan Maxson's user avatar

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