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12 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 ...
wzkchem5's user avatar
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12 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 ...
Nike Dattani - No Free Time's user avatar
10 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 ...
Tyberius's user avatar
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9 votes
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Are thermostat parameters transferable between AIMD and classical MD?

Yes, provided the nature and timescales of the dynamics are the same it should be safe to use the same thermostat (and time-step, barostat etc) parameters for the ab initio MD and the classical MD. ...
Phil Hasnip's user avatar
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9 votes
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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 ...
Andrew Rosen's user avatar
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8 votes
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Is AIMD classified as MD or DFT?

Purely classical MD would use a classical forcefield to do MD, whereas ab initio MD (AIMD) would usually involve DFT calculations to obtain the forces, then the same type of MD procedure can be used ...
Nike Dattani - No Free Time's user avatar
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 ...
Pranav kumar's user avatar
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7 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 ...
mykd's user avatar
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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 ...
Nike Dattani - No Free Time's user avatar
7 votes
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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 ...
wzkchem5's user avatar
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6 votes
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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 ...
Nike Dattani - No Free Time'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
  • 8,142
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
5 votes

Is AIMD classified as MD or DFT?

Ab initio molecular dynamics (AIMD) involves both ab initio and molecular dynamics (MD). If the ab initio is done by density functional theory (DFT), the method is both a density functional and MD ...
Susi Lehtola's user avatar
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5 votes
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Choice of SMASS for AIMD simulations in VASP

If you are on VASP, there is a script from Qijing Zheng to whom goes the credit, with this script you can estimate the value of SMASS. Just in case you can't access that, I am leaving you the script ...
Jaafar Mehrez's user avatar
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 ...
Cody Aldaz's user avatar
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4 votes
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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 ...
mykd's user avatar
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3 votes
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How to simulate the electron transfer during OER with AIMD?

When a bias is applied to an electrode that drives OER, the bias is versus a counter electrode. The counter electrode is a macroscopic distance away, and I have yet to see an AIMD simulation that ...
Andrey Poletayev's user avatar
3 votes
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Discrepancy in forces between AIMD and relaxation

This is a bad EDIFF for what you are trying to do I suspect. Your forces will not be converged to the same value that your energies are converged to since the forces are the gradient of energy. If ...
Tristan Maxson's user avatar
3 votes
Accepted

Average value of lattice parameters from cell trajectory

This python code should work. It will print the average lattice parameters from the file Si.cel. ...
Abdul Muhaymin -Free Palestine's user avatar
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 ...
Tyberius's user avatar
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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, # ...
taciteloquence's 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.
nisarmuhammad131's 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 ...
DoubleKx's user avatar
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2 votes
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Equilibrating Surface Temperature Through NVT Ensemble Ab Initio Molecular Dynamics

"Ensemble" is a pretty strong word for a system with fewer atoms than the cards in a poker deck of cards. The Nose-Hoover thermostat attempts to redistribute energy between a system's ...
Shern Ren Tee's user avatar
2 votes
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Controlling Initial Velocities in NVE Trajectory Simulations with VASP

As I understand in your question, you want to perform AIMD with NVE ensemble. Based on VASP documentation, it is recommened to set MDALGO=1 and ...
Jaafar Mehrez's user avatar
1 vote
Accepted

Geometry of H2O in the v=1 vibrational state for AIMD simulation

"Geometry" is complicated in quantum mechanics, because we have probability distributions rather than precise geometrical positions as we would have in classical mechanics. If we make the ...
Nike Dattani - No Free Time's user avatar
1 vote

Absorption enthaply at different temprature in VASP software via ab initio molecular dynamics

I will give a general outline on how to perform such caculation. Before we start with the AIMD calculations we need to find the perferred adsorption site/sites according to the following steps: ...
Jaafar Mehrez's user avatar
1 vote
Accepted

Steps to obtain ionic diffusivity using AIMD

Here is an example from vaspwiki
Binh Thien's user avatar
  • 2,137

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