Questions tagged [aimd]
Questions about ab-initio molecular dynamics (AIMD).
20
questions
2
votes
0
answers
29
views
How to estimate the minimal distance between atoms for which a pseudopotential-based AIMD gets forces correctly?
I am doing ab initio molecular dynamics in VASP. As far as I know, pseudopotentials approximate all-electron potential far from the nucleus, and deviate from it near the nucleus.
When some of my atoms ...
1
vote
0
answers
36
views
Problem with CP2K running AIMD
I have met serious problem with cp2k running AIMD. I complied CP2K 2023.1 with gcc.9.3.0 and intelmpi. First, I ran the test1.inp file (https://1drv.ms/u/s!AtO91yh6_pLhg51bJVuIJt7N4ZZU7w?e=YtB3ZC) and ...
- 305
2
votes
0
answers
18
views
AIMD simulation of a silica slab and a electrolyte placed in the vacuum region
Can someone share a VASP input file as a template that I can use to equillibrate a system as mentioned in the title. I created one but I am not sure if that is correct or not.
...
- 481
1
vote
0
answers
32
views
How to calculate constraint force for angle constraint in CP2K NVT MD simulation?
I am running a CP2K NVT molecular dynamics simulation and want to apply an angle constraint between three atoms. In my previous simulations, I used a bond constraint between two atoms, and it was easy ...
- 1,561
4
votes
1
answer
111
views
Are thermostat parameters transferable between AIMD and classical MD?
I need to run several large systems using AIMD. I would like to benchmark same phase transition phenomenon using different thermostats (like Nose vs Langevin). For that it is crucial that I pick most ...
- 481
5
votes
1
answer
82
views
How to simulate the electron transfer during OER with AIMD?
I am trying to simulate the electron transfer from adsorbed H2O molecule to the electrode with AIMD. I guess I need to set up an external electric field, so the electron inside the H2O molecule would ...
- 1,938
3
votes
1
answer
99
views
Discrepancy in forces between AIMD and relaxation
I am a bit perplexed to see substantive differences in forces (as taken from OUTCAR with ASE) computed when I take AIMD frames and run static electronic relaxations on each one (no additional ionic ...
- 763
5
votes
2
answers
732
views
Is AIMD classified as MD or DFT?
As far as I know, we need force fields such as Tersoff/Coulomb potentials when performing MD simulations. In AIMD, we use pseudopotentials similar to DFT.
Which method should we classify AIMD to: a ...
- 2,025
4
votes
0
answers
171
views
Regarding use of GCMC to add water molecules
I am working on a goethite system, and wish to fill the unit cell with water molecules for AIMD simulation using quantum espresso. For this, some papers[1],[2] indicated the use of Grand Canonical ...
- 871
7
votes
1
answer
256
views
Simulating autoionization of small molecules using DFT or AIMD
From what I'm reading, simulation of auto-ionization in liquid substances is hard to do using gas phase DFT or AIMD [1][2][3]. I am using ORCA to do my work and I must confess that I'm shocked to see ...
- 327
4
votes
1
answer
1k
views
Why does the temperature fluctuate severely during the AIMD using an NVT ensemble?
I am trying to raise the temperature of my model and keep the temperature at 300K, with an NVT ensemble and Nose-Hoover thermostat.
I am doing this job with VASP, here is the ...
- 1,938
11
votes
1
answer
381
views
Steps to obtain ionic diffusivity using AIMD
I read a paper and the authors wrote they use AIMD to estimate the ionic diffusivity of materials. I wonder steps to obtain the value at different temperatures. What are the input and output of ...
- 2,025
11
votes
1
answer
232
views
How would one find a material's equilibrium structure at any specific temperature?
Let's take an example of a simple FCC material, a binary alloy. Above absolute zero K, the alloy will start to disorder and become an FCC solid solution. The alloy would develop defects as it ...
- 5,125
7
votes
2
answers
265
views
What is the real reason behind the minimization of the system at the beginning of a Car-Parrinello MD calculation?
I've been studying MD and more specifically about Car-Parrinello Molecular Dynamics and I'm not entirely sure if I understood the meaning behind the minimization.
This is the way I understand it: The ...
7
votes
2
answers
160
views
How to take periodic snapshots while running a simulation in VASP?
Same question, rephrased:
What is the procedure to take snapshots at fixed intervals while running an AIMD or DFT Simulation in VASP?
OR
Which parameter in the INCAR file do I modify to achieve ...
- 1,237
13
votes
0
answers
564
views
How to build amorphous Al2O3 using the AIMD method implemented in VASP?
I want to build amorphous $\ce{Al_2O_3}$ with the AIMD (ab initio molecular dynamics) method implemented in VASP.
I'm thinking of this process in three steps:
Build initial supercell
Melt
Quench
I ...
- 14.8k
10
votes
2
answers
427
views
Choosing RAM, CPU time, # of cores, and other parameters for an MD run
I did an AIMD run in VASP using 64 cores (32 cores/node) and 250 GB of memory (125 GB/node) for 5 ps (1 fs time step). The calculation took 12.6 hours to complete. CPU efficiency was 99.7% and memory ...
- 1,050
9
votes
1
answer
1k
views
AIMD and velocity scaling in VASP
Typically one does velocity scaling to "heat" their sample with MD.
How do we do this in VASP? Is it by setting the SMASS=-1 and ...
- 1,050
10
votes
2
answers
266
views
What are some methods for modeling bulk phase infrared spectra?
I am interested in predicting the infrared spectra of bulk phase molecules, it seems that AIMD (ab initio molecular dynamics) is the current best approach. I have found a tutorial on using CP2K to do ...
- 1,212
19
votes
3
answers
2k
views
What are the types of ab initio Molecular Dynamics?
I am new to the world of Molecular Dynamics, and am curious to know exactly what is considered to be an ab initio Molecular Dynamics (AIMD) method, and how do they work?
The seminal work by Roberto ...
- 4,677