Questions tagged [molecular-dynamics]
For questions related to the use of or theory behind classical or ab initio molecular dynamics.
54
questions
8
votes
1answer
26 views
Using the VACF command in LAMMPS to get the velocity autocorrelation function
I am writing a simple Lennard-Jones fluid simulation in LAMMPS.
So far, I have outputted the temperature, volume, density, total energy, enthalpy, pressure, and all of it seems to be believable every ...
7
votes
0answers
44 views
How to do molecular dynamics calculations and analyse trajectories of small molecules?
I need to perform some MD calculations and then trajectories of some small molecules analyzed.
What I have is
protein
cofactor (FAD)
small molecule (either single O2 molecule or single Chlorine atom)
...
9
votes
1answer
127 views
Can I compute the free energy difference in (temporally) nearby micro-states using the Zwanzig equation for Free Energy Perturbation?
I wanted to understand the Free Energy Perturbation in an NVT ensemble.
Wikipedia explains it as:
$$
\tag{1}
\Delta F = F_1 - F_0 = -\kappa T \ln \left<\exp\left( \frac{-(E_1-E_0)}{\kappa T}\right)...
19
votes
2answers
631 views
Does increasing Lennard-Jones cutoff means higher accuracy?
I am currently trying to simulate a large box of QM/MM water molecules with SPC/Fw model and GGA DFT functional (a cube of 40 angstrom sides). To validate the QM and MM simulations separately, I am ...
11
votes
1answer
82 views
Modelling Diffusion of Molecules Through a Physical Barrier
I would like to model the diffusion of various small molecules (e.g. $\ce{O2}$, $\ce{H2O}$, $\ce{MeOH}$, etc.) through polymeric barrier material (e.g. polyethylene, ethylene vinyl alcohol, ...
7
votes
1answer
117 views
Does the Hamiltonian of an unbiased simulation change when the simulation moves from a stable basin to another?
I wanted to understand the change in the Hamiltonian function as an unbiased simulation goes from one stable basin to the other.
Does the Hamiltonian stay constant or does it change as the unbiased ...
14
votes
3answers
399 views
References for Molecular Dynamics?
I am new to the world of Molecular Dynamics (zero practical experience), and I know that a starting point to really go into the back-bone of MD is Statistical Mechanics (took a semester course in ...
8
votes
1answer
90 views
What is the “overcoherence problem” in Ehrenfest dynamics?
I am a novice in Ehrenfest dynamics and would like to know why Ehrenfest dynamics suffers from the "overcoherence problem"?
5
votes
0answers
43 views
What is the difference between Ehrenfest dynamics and Born-Oppenheimer Molecular Dynamics? [duplicate]
What is the fundamental difference(s) between Ehrenfest dynamics and Born-Oppenheimer MD? Also, in what situation(s) or case(s) one is preferred than the other one?
11
votes
0answers
68 views
Calculate free energy for a canonical (NVT) ensemble [closed]
I have an NVT ensemble of water molecules (liquid) and I want to calculate the Free energy (helmholtz or gibbs) whichever is equivalent to the following relation:
$$ \Delta F = -RTlnQ $$
I can't ...
10
votes
2answers
230 views
What are the factors to consider before docking 2 proteins?
With no background in biological science, I need help with docking 2 proteins together. This issue is with regards to SARS-CoV-2. The 2 proteins are Spike glycoprotein and membrane protein. What are ...
7
votes
0answers
22 views
Setting multiple new atype/dtype/itype with LAMMPS fix bond/create
When creating a new bond in a LAMMPS simulation with the command fix/bond create it is likely new angles/dihedrals/impropers be need to be set. This can be done with the atype/dtype/itype arguments ...
10
votes
1answer
46 views
What does the Neighbor command do in LAMMPS?
I frequently see LAMMPS codes, and almost all of them have the neighbor 0.5 bin command. I completely studied the LAMMPS manual for the neighbour command and did ...
5
votes
1answer
61 views
Why am I losing bonds when I use PACKMOL on two proteins?
I recently started using PACKMOL to pack a few proteins together. I wrote this PACKMOL code:
...
11
votes
1answer
44 views
LAMMPS code that I wrote not behaving as expected. Some issue with the group & region commands
I am actually working on SARS-CoV-2 proteins. Specifically I am trying to tribologically disengage the Spike Glycoprotein from the Membrane protein using LAMMPS. The method is to use amorphous carbon ...
6
votes
0answers
36 views
What are the types of Quantum Molecular Dynamics (QMD)?
In similar spirit to recent questions on Quantum Monte Carlo, ab-initio Molecular Dynamics, types of scf, among others, I now ask:
What are the types of Quantum Molecular Dynamics (QMD)?
What are ...
8
votes
0answers
30 views
Sample LAMMPS file for graphene growth on a metal surface
I am working with graphene growth on metal substrates. But I need some sample codes to know if I am doing it in the right way because running multiple simulations in LAMMPS takes a lot of time. Can ...
10
votes
1answer
79 views
How can I calculate the Poisson ratio of an amorphous material with LAMMPS?
I noticed that we can calculate the Poisson ratio of a crystalline metals with LAMMPS. I wonder if we can use that example for a metallic glass! If no, is there any other way, with another software?
11
votes
1answer
99 views
Dealing with symmetry of ordered primitive cell during DFT structure relaxation
I have a large disordered cubic structure that I would like to do AIMD on to look at cation diffusion. I found the primitive cell and then ordered it to create several configurations. I will then ...
9
votes
0answers
57 views
I wrote a Python code to do MD for a Lennard-Jones fluid but the VACF is wrong: What might be the problem? [closed]
I am trying to write a molecular dynamics simulation for a Lennard-Jones fluid in a box with periodic boundary conditions. The box has no net momentum. I am writing this in python.
I have written a ...
11
votes
1answer
59 views
Calculating diffusion coefficient from Mean Squared Displacement
I am performing a molecular dynamics simulation and I have calculated the velocity autocorrelation function (VACF), $\psi (t)$ and mean square displacement, $\langle (\Delta r)^2 \rangle$. In my ...
10
votes
2answers
160 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 ...
8
votes
1answer
137 views
Are there any MD packages that do proper free energy sampling in the NPT ensemble?
Statistical Mechanics is the basis of molecular level calculations of properties and averages. Nowadays free energy calculations are fairly "turn-the-crank", which is not necessarily a good ...
17
votes
3answers
401 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 ...
15
votes
0answers
67 views
Quadrature over three Euler Angles for orientation averaging
Does anybody know about an accurate quadrature rule over three Euler angles $\theta, \phi, \chi$?
I am trying to calculate the average value of an arbitrary function $f(\theta, \phi, \chi)$ for a ...
14
votes
1answer
182 views
Ab initio molecular dynamics to check material stability at finite temperature
I completed an ab initio molecular dynamic (AIMD) simulation in VASP for a hypothetical material. The simulation was done for 5ps with 1fs steps and the temperature was set to 300K using Nosé–Hoover ...
6
votes
0answers
46 views
How do I generate an aluminum force-field for a LAMMPS input file? [closed]
I have been assigned a project on the generation of a force-field of Al (aluminum) for a LAMMPS potential.
I have no idea how to proceed and what to do next. Can anyone please let me know how should I ...
19
votes
1answer
112 views
Why can't I reproduce the behavior of an H-saturated graphene flake?
I'm trying to simulate a graphene flake with its edge C atoms saturated by H atoms, in a temperature ramp from 300 K to 1600 K, using LAMMPS and the AIREBO potential proposed by Stuart et al. in 2000.
...
12
votes
0answers
61 views
Poiseuille flow by LAMMPS [closed]
I am trying to model 3D Poiseuille flow of an argon gas confined between two parallel platinum plates by using LAMMPS. I have one reference paper, as given in [1] below. I built my platinum structure ...
12
votes
1answer
408 views
How to rectify the error “Lost atoms: original 28437 current 3659” in LAMMPS?
I have modeled a complex structure of a protein and a Carbon nano-cone (used as an indenter to the protein) using PACKMOL. The LAMMPS data file of the complex structure consists of 4 atom types (C O N ...
11
votes
1answer
72 views
3D Poisson equation solver for arbitrary charge distribution?
I am trying to compute the electrostatic potential profile from a distribution of point-charges that were output from an MD simulation. Does anyone know of ready-made Poisson solver packages that are ...
14
votes
1answer
115 views
What are the ways to ensure thermodynamic stability of a DFT modelled new structure?
One way of predicting the thermodynamic stability of a DFT modelled structure is to calculate the energy above convex hull, which was used as the criterion in The Materials Project database. For ...
18
votes
5answers
1k views
Molecular Dynamics simulation software for Windows
Is there a Windows-based Molecular Dynamics simulation software which is easy to use?
10
votes
1answer
44 views
Can you model Radiation Chemistry with existing MD software?
I'm wondering if it is possible to simulate the chemical changes materials undergo when exposed to ionizing radiation for a finite period of time with Molecular Dynamics (MD) software. In principal ...
8
votes
1answer
108 views
Is it possible to use the Parrinello-Rahman barostat for NPT simulations in CP2K?
It is possible to use different types of thermostats in CP2K by specifying them in the corresponding section of the input as mentioned here. But there is no mention of specifying the barostat type in ...
18
votes
1answer
213 views
How to optimize zinc oxide bulk structure at certain pressure with LAMMPS
I am trying to simulate the Zinc oxide bulk structure (periodic) at constant pressure(0.0 ~ 20.0 GPa) to observe phase transition with LAMMPS.
However, I approached a problem that the fluctuating ...
23
votes
2answers
2k views
What are the “smart algorithms” applied to solve the “curse of dimensionality”?
The "curse of dimensionality" is an ubiquitous issue arising in both electronic structure and quantum molecular dynamics, which refers to the exponential scaling of computational cost with ...
19
votes
2answers
109 views
How to choose replica exchange interval?
I was wondering what goes into the consideration of choosing the frequency to attempt swaps for replica exchange? D. Sindhikara, 2008 proposes the faster the better, but this goes against the view ...
15
votes
1answer
134 views
Why do interaction potential parametrizations of bulk systems not work for corresponding nano-systems?
I am studying several thermodynamics properties of crystalline iron oxides ($\ce{Fe3O4}$, $\gamma-\ce{Fe2O3}$) in their solid phases by MD simulations. At the moment, I am facing many difficulties in ...
12
votes
1answer
50 views
Rule-of-thumb for Morse potential cutoff in molecular dynamics?
Is there a rule-of-thumb for selecting a cutoff for the Morse potential in molecular dynamics simulation? For instance, is it typically some multiple of the equilibrium distance?
20
votes
3answers
128 views
Simulating breaking bonds in molecular dynamics
How does one introduce the possibility of breaking a bond in a molecule during MD simulation?
I only found the cases when we just introduce the harmonic potential $U_{ij} = \frac{1}{2}k(r_i - r_j)^2$ ...
14
votes
1answer
71 views
Can Newton's Equation of Motion be Integrated Analytically for Certain Chemical Systems?
In molecular dynamics, one typically integrates Newton's equation of motion, for example using a leap-frog algorithm. Are there chemical systems, for which an analytic integration is a viable ...
14
votes
1answer
101 views
Modeling vibronic interaction beyond Born-Oppenheimer
Within Born-Oppenheimer approximation, the motion of atomic nuclei are considered as being separated from the electrons movement. Although in general this approximation is valid for a high number of ...
14
votes
1answer
75 views
How can I decide on the order of different monomers in a co-polymer?
While performing molecular dynamics simulations on a co-polymer, how long should the minimum size of the polymer be, to replicate the experimental properties with a reasonable error?
Within this ...
14
votes
2answers
150 views
What are the parameters that need to be calculated to design the structure of a molecule?
Before performing Molecular Dynamics on a co-polymer that doesn't have a ready-to-use structure anywhere, the monomer fragment was built in Avogadro software with 0 net charge, B3LYP theory and 6-31G(...
33
votes
2answers
200 views
How should one choose the time step in a molecular dynamics integration?
Choosing too small of a timestep leads to an unrealistic simulation time, whereas too big of a timestep leads to the system not being represented correctly (or, in the case of an algorithm like SHAKE, ...
11
votes
1answer
182 views
What are good resources to learn Materials Modeling? [closed]
I wonder if there are any books or resources to start learning Materials modelling using methods
density functional theory
quantum monte carlo
molecular dynamics
12
votes
1answer
77 views
Computing phonon dispersion from molecular dynamics simulations?
How would one obtain the phonon dispersion curve from a molecular dynamics simulation trajectory? What are the steps involved? Are there any packages that does this? If so, please mention them.
28
votes
2answers
204 views
Machine learning interatomic potentials for molecular dynamic simulations: are they good?
I know the general question of machine learning in computational chemistry has been already raised here: What is the current status of machine learning applied to materials or molecular systems?
...
15
votes
3answers
91 views
Does anyone know any software for MD simulation which include the effect of magnetic field?
I am interested to generate some configurations from MD simulations which include the presence of strong magnetic field. Does anyone know any software that has some functionality to do this?
