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3 votes
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LAMMPS: Start NVE simulation with different initial energies

I am new to LAMMPS and am using it to conduct microcanonical (NVE) MD simulations. I am able to run NVE simulations using the fix NVE command, but I want to start a series of simulations in parallel ...
KugelBlitz's user avatar
3 votes
1 answer
183 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 ...
Hadeel Moustafa's user avatar
4 votes
2 answers
315 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 ...
Pranoy Ray's user avatar
  • 1,637
4 votes
1 answer
125 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?
Surya's user avatar
  • 101
2 votes
0 answers
59 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 ...
user366312's user avatar
  • 2,556
3 votes
1 answer
302 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.
Madeleine Fisher's user avatar
3 votes
1 answer
119 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 ...
lzzard's user avatar
  • 123
2 votes
1 answer
74 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' ...
Pranoy Ray's user avatar
  • 1,637
5 votes
1 answer
576 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 (...
diamond999's user avatar
3 votes
1 answer
138 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 ...
Devanjith Fonseka's user avatar
5 votes
0 answers
351 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 ...
user avatar
5 votes
1 answer
101 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 ...
user366312's user avatar
  • 2,556
3 votes
1 answer
80 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 ...
user366312's user avatar
  • 2,556
3 votes
1 answer
403 views

Where can I find this formula?

I found this source code written by someone: ...
user366312's user avatar
  • 2,556
4 votes
0 answers
62 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....
user366312's user avatar
  • 2,556
1 vote
1 answer
254 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. ...
Abhinav Srivastava's user avatar
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....
sarra6's user avatar
  • 579