Questions tagged [energy]
The energy tag has no usage guidance.
16
questions
3
votes
1
answer
155
views
Is a D-Wave quantum computer able to do TD-DFT calculations?
I was reading this paper (Computing molecular excited states on a D‑Wave quantum annealer) and wondering if I can make a QUBO model for the equations used in the TD-DFT energy calculation for the ...
4
votes
2
answers
230
views
Can the the relaxed energy of a material system (eV/atom) computed by DFT using VASP be positive?
If it is positive, why is it so? Is it due to specific convergence criteria or choice of pseudopotentials? I cannot check the convergence of the DFT calculations as they have been downloaded from a ...
- 1,481
4
votes
1
answer
86
views
Can adsorption energy be upto -8 eV for VOC adsorption in MoS2 layer?
I've been using VASP for DFT calculations and came across with an adsorption energy value over $-8\,eV$.
Is this a reasonable value for S-H bond?
- 101
2
votes
0
answers
55
views
Method for Energy Computation of Protein Structures
So far i have found only one paper that describes how we can compute protein energy while doing MD simulation:
Nishikawa, Ken, Motohisa Oobatake, and Tatsuo Ooi. "Method for Energy Computation ...
- 2,352
3
votes
1
answer
154
views
Calculating Reorganisation energy using ORCA
I wondered if anyone knows of a way to calculate the reorganization energy of a molecule utilizing orca 5.0.3.
3
votes
1
answer
58
views
Theoretical Capacity of g-C3N4?
I was reading a paper that stated:
For example, graphitic carbon nitride (g-C3N4) is considered a potential anode material for lithium ion batteries due to its easy accessibility, low cost and large ...
- 53
2
votes
1
answer
50
views
A cubic unit cell in DFT of volume 'V' has 'n' atoms in it, for an extended volume V' how many atoms would be there in the new volume?
We can also assume the lattice parameter of the cubic unit cell to be a and the that of the extended cell to be a', which means that V' = (a')^3
So is the number of atoms n' in the extended volume V' ...
- 1,481
5
votes
1
answer
309
views
How to plot HOMO-LUMO diagram using python?
I'm trying to create a HOMO-LUMO diagram for a presentation, similar to the below figure from ResearchGate. I would like to learn how to do this with Python if possible, since I know this language (...
- 835
3
votes
1
answer
104
views
Energy balance in a molecular dynamics simulation with ghost atoms and periodic boundary conditions?
I am performing a simulation in LAMMPS with granules (DEM) and I had a question regarding the conservation of energy. If an interaction happens where one granule is in the simulation box and the other ...
5
votes
0
answers
245
views
Is there an effective way to get the energy of a system from a MD trajectory in postprocessing? [closed]
I am trying to get the potential energy of a system at each frame of a molecular dynamics trajectory after running the simulation. My current approach is as follows:
Use MDAnalysis to iterate through ...
mertvy
5
votes
1
answer
96
views
Why do we need to find minimum energy in a protein chain?
High–quality protein backbone reconstruction from alpha carbons using Gaussian mixture models
The above research paper is about a software tool for reconstructing a protein's main chain model only ...
- 2,352
3
votes
1
answer
69
views
What formula should I use to calculate the total energy of a linear polymer chain?
I am using the Bead-spring model to model a polymer chain.
Suppose, the polymer has 3 monomers in its chain:
$$\ce{A1-A2-A3}$$
And,
I can use the following formula to calculate the total Lennard-Jones ...
- 2,352
3
votes
1
answer
401
views
4
votes
0
answers
61
views
Where should I apply the harmonic spring function in the case of polymer simulation? [closed]
I need to simulate the off-lattice movement of a polymer chain in a 3D space using Monte Carlo simulation. Note this is not a simulation of polymer growth; rather this is about polymer movement/motion....
- 2,352
1
vote
1
answer
162
views
Exporting IFD output to poseviewer file
I have an output from induced fit docking (IFD) in Maestro.
I want to calculate the MM-GBSA for the output obtained from IFD in Maestro (Schrodinger) for which poseviewer file (.pv.maegz) is required.
...
8
votes
0
answers
53
views
The effect of different mediums on the molecular orbital energies [closed]
I want to study the effect of different mediums, gas and various solvents, on the energy of the 10th highest molecular orbital of multiple quinones, which I obtained by a Gaussian software calculation....
- 527