Hot answers tagged

11 votes

What are the types of ab initio Molecular Dynamics?

CPMD: Car-Parrinello Molecular Dynamics An approximation of BOMD (Born-Oppenheimer MD) where fictitious dynamics is used on the electrons to keep them close to their ground state, so that we do not ...
user avatar
  • 27.8k
9 votes
Accepted

How to take periodic snapshots while running a simulation in VASP?

There is no way to do this directly in VASP, but you can achieve this goal using the Atomic Simulation Environment (ASE). With your OUTCAR available, do the ...
user avatar
  • 6,852
8 votes
Accepted

Simulating autoionization of small molecules using DFT or AIMD

This is because autoionization is very thermodynamically unfavored near room temperature. I don't know much about water in a water-DMSO mixture, but let's take pure water as an example. The ...
user avatar
  • 6,408
7 votes

What are the types of ab initio Molecular Dynamics?

2nd Generation CPMD Car-Parrinello MD avoids repeatedly solving the electronic problem by propagating the orbitals as if they were particles governed by Newton's equations. This is much more efficient ...
user avatar
  • 13.9k
7 votes

How would one find a material's equilibrium structure at any specific temperature?

You mentioned DFT, which is typically used to calculate the electronic energy at zero temperature. You can adjust the geometry until this electronic energy is lowest, but then you might ask why for a ...
user avatar
  • 27.8k
7 votes

How to take periodic snapshots while running a simulation in VASP?

In can be done easily using python or bash script. You have to keep looking for changes in OSZICAR. Whenever OSZICAR prints 'F' i.e. end of electronic self ...
user avatar
  • 3,054
7 votes
Accepted

Why does the temperature fluctuate severely during the AIMD using an NVT ensemble?

The primary reason is that your simulation time is too short. To thermally equilibrate a system, the simulation time must be much longer than the period of the slowest phonon mode, so that even the ...
user avatar
  • 6,408
6 votes
Accepted

What is the real reason behind the minimization of the system at the beginning of a Car-Parrinello MD calculation?

I explained Car-Parrinello MD here, and a key point is that it approximates BOMD (Born-Oppenheimer Molecular Dynamics) where the electronic state is minimized (i.e. the ground electronic state is ...
user avatar
  • 27.8k
6 votes

What are the types of ab initio Molecular Dynamics?

ab initio Ehrenfest Dynamics From Li et.al.,2005, JCP "The Born Oppenheimer (BO) and extended Lagrangian (EL) trajectories are founded on the assumption that a single electronic potential surface ...
user avatar
  • 1,940
5 votes

What is the real reason behind the minimization of the system at the beginning of a Car-Parrinello MD calculation?

Yes your understanding is correct. It helps to think about BOMD as classical dynamics. The electrons are the springs that hold the masses together and the nuclei are the masses.The two key terms are ...
user avatar
  • 7,744
4 votes
Accepted

What are some methods for modeling bulk phase infrared spectra?

Vibrational maps and density of states In water AIMD community, to avoid excessively heavy calculations of molecular moments, researchers use velocity autocorrelation function (which converge much ...
user avatar
  • 1,940
3 votes

What are some methods for modeling bulk phase infrared spectra?

I'm not an expert in MD/AIMD software so I can really only discuss methods rather than an actual workflow/software that can carry it out. One approach that has been explored for accelerating AIMD and ...
user avatar
  • 13.9k
3 votes

Choosing RAM, CPU time, # of cores, and other parameters for an MD run

This won't directly answer your question, but a note of caution about focusing too much on optimization. It's definitely worth doing some experimentation to find an efficient combination of memory, # ...
user avatar
2 votes

Choosing RAM, CPU time, # of cores, and other parameters for an MD run

For MD I recommend The Gamma Cantered KPOINTS with Grid mesh 1 1 1.
user avatar
2 votes

AIMD and velocity scaling in VASP

I think I figured out parts of my question. But would really benefit from a VASP/AIMD expert weighing in. This appears to be the correct way of doing velocity scaling in VASP. And you can scale the ...
user avatar
  • 1,040
1 vote
Accepted

Steps to obtain ionic diffusivity using AIMD

Here is an example from vaspwiki
user avatar
  • 1,450

Only top scored, non community-wiki answers of a minimum length are eligible