# All Questions

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### Reading DCD files using Python without using third party packages?

I am trying to read a NAMD DCD file using Python. Following the code given at here to read DCD files using Fortran, I have written the following code snippet to read the header section of the DCD file....
1 vote
14 views

### Gromacs simulation with 100 copies of same ligand appears weird

I'm a gromacs noob, so I appreciate your patience. I tried simulating the interaction of a protein with 100 copies of the same ligand, in water. The workflow I used is attached here as a picture. The ...
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1 vote
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### What is the difference between relax and multiple scf calculation in Quantum ESPRESSO?

Relaxation calculation gives us the ionic position of the relaxed structure. Now instead of doing a relaxation calculation, if I do fixed point self-consistent field (scf) calculation for varying ...
1 vote
13 views

### ASE: Receiving error on implimenting ase cellpar_to_cell method

I am getting the following error while implementing ase cell method. I am not able to understand where is it going wrong, although I think it has to do something with the values I am getting for cell. ...
• 115
40 views

### Choosing the right basis set for describing vdW-interactions with DFT-D3

I want to do some DFT calculations for structures of protonated alkaloid dimers. I know that a method of choice when vdW interactions are involved is the use of dispersion corrections. But now I am ...
• 489
205 views

### Change cif file into vesta format

I have 100 .cif files. I want to convert them all to .vesta files through vesta software (https://jp-minerals.org/vesta/en/download.html). I know I can choose them one by one and convert them. Is ...
• 61
62 views

### Density Functional Perturbation Theory

What is the difference between density functional perturbation theory (DFPT) and many-body perturbation theory (MBPT)? Also, please help me understand why approximations like PBEsol are considered as ...
• 375
953 views

### How can I run my calculations on a remote server?

I'm going to use a more powerful server to run my simulations on it using a remote control software (The server is in another building). It's my first time to try that. What are the things that I ...
• 855
24 views

### Comparing stability of phases under constant pressure

I have used DFT to calculate the internal energy of a couple of different phases at 0K. As I would also like to compare the relative stability of the phases at finite temperature, I have also computed ...
26 views

### Compositional SMILES data

I am interested to know if it is possible to encode compositional information in SMILES strings or other structural identifiers. For instance, in generating a SMILES string when combining two ...
18 views

### How are reconstructed surfaces named?

I am trying to understand the terminology of reconstructed surfaces. Simple surfaces such as 2x2 or 1x1 make sense to me. For instance, figure 1 of the paper https://doi.org/10.1063/1.1574798 shows a ...
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531 views

### Why does my zincblende structure not look cubic?

The structure of my material is zincblende. So normally the structure is cubic. However, when I open the primitive cell with xcrysden it dosen't look 100% cubic. It's a little bit inclined. Also when ...
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44 views

### When and why are torques needed in molecular dynamics simulations?

I have seen that many MD simulations compute the torques due to dipole-dipole interactions and other interactions. I understand that there is a torque on a dipole in an electric field. I don't ...
• 3,299
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### How to change cell shape during calculations in LAMMPS?

I was doing some calculations using LAMMPS and wondered if there was a way to change the cell shape during npt or nvt calculations (in the latter, changing the cell shape while keeping the volume ...
• 689
24 views

### Why do I get very intense picks when I use PBE0 with NC PP?

I used PBE0 to get projected density of states using norm-conserving pseudopotentials with Quantum ESPRESSO. I found very intense picks (scf -> projwfc ) compared to the ones that I found using ...
• 855
31 views

### NEB calculations in VASP

In NEB calculations, I am getting much higher energy values. ...
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### How do I get openMPI to run with gromacs?

When I run the command mpirun -np 48 mdrun_mpi -deffnm md -v, the software works with no error, but it only runs as fast as when I'm using 1 CPU (the computer I'm ...
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60 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 ...
52 views

### Absorption spectra with Gaussian

I want to calculate the absorption spectra of molecules (and possibly ions) with TD-DFT. I have used Gaussian in the past and, to my knowledge, the application of TD-DFT is implemented in this code. ...
• 689
120 views

### Extracting band structure data using Boltztrap for Quantum ESPRESSO

I used PBE0 in my calculations using Quantum ESPRESSO . I have ran a scf calculation then I used Boltztrap by running the command btp2 -vv interpolate -m 3 ./ then <...
• 855
279 views

### Using OpenBabel's gen3d in a Python notebook

I want to preface this by saying I am really new to computational chemistry and this kind of programming in general, but I am having real trouble figuring out how to use OpenBabel's ...
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155 views

### Constrained optimisation on a hypersphere

I am currently trying to implement a GS2 (Gonzalez-Schlegel second order) IRC algorithm in a python code. I am following the original paper ref(1). The main problem is in the constrained optimisation ...
• 6,216
83 views

### Layer detection in a crystal structure

Context I have two images from a Monte Carlo Basin Hopping where silicon (in yellow) is getting replaced by germanium (in blue). Both have 32 germanium atoms at Si/Ge = 2.5; only the Ge distribution ...
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78 views

### How can I transform my unit cell positions to cartesian coordinates?

I have a structure with the parameters bellow: ...
• 855
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### How can I build the wheels necessary for a quick installation of PySCFad on a "compute node"?

The following is the procedure I have been following: Install PySCFad ...
• 30.9k
220 views

### Can someone guide me on how to get the k-point file for a VASP simulation?

I have a system with box dimensions of 21.0 * 21.0 * 80.0 for x,y and z directions. How may I generate the KPOINTs mesh for this system for VASP simulation? Any reference on this is hugely appreciated....
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45 views

### Any software that can model eddy currents?

Is there any software on metals that can predicts orbital or induced currents in metals in the presence of a magnetic field or electromagnetic waves?
• 332
71 views

### VASP with VDW dispersion corrections for a large system

I have been trying to find the binding energy of a water molecule with a crystalline silica slab and want to use vasp. whenever I try to use vasp for this purpose i get this error. Also, can someone ...
• 101
85 views

### Calculate deprotonation energy or Gibbs free energy of acids

I'm delving into the world of superacids, acids with an acid strength greater than that of sulfuric acid at 100%. I've recently encountered some computational papers which suggest that the ...
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236 views

### How to model an isolated molecule with Quantum ESPRESSO?

I am trying to model isolated structures such as quantum dots or molecules in Quantum ESPRESSO (QE). QE uses 3D periodic boundary conditions (PBC) by default. That's why in order to reduce any ...
31 views

### How to add the scissor operator in Quantum ESPRESSO input?

I want to calculate the optical, transport and electronic properties of my material. GGA underestimate the bandgap. I tried GGA+U but the bandgap is still underestimated and also when I tried to use ...
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51 views

### Calculation of Carbon Quantum Dots using Quantum ESPRESSO

I have build a carbon quantum dots model based on this paper. The model looks like this. I have calculated the density of states of the system, but does not get a desired plot as written on the paper,...
20 views

### Using LAMMPS and VMD to analyze a new structure

I have a new structure that I want to analyze (lets just call it a shape). For the shape, I have the coordinates that make it up. I even have a tcl script in VMD that allows me to create the shape ...
166 views

### Which Python packages, APIs or online databases may be used for a Python script to find bond dissociation energy between two arbitrary atoms?

Let us say that I wish to create a function that may do the following: >>> find_bond_energy(atom1="C", atom2="O", order=3) 1072 kJ/mol ...
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### Where can I find the MASTANI-2014 tutorial files?

There was a two-week summer school on Density Functional Theory using Quantum ESPRESSO in the summer of 2014 organized by The Abdus Salam International Centre for Theoretical Physics (ICTP), jointly ...
72 views

### Unexpected atoms while working with XYZ files in rdkit

I am processing some XYZ files using the rdkit library in python. I came across some strange/unexpected behaviour. Consider a sample XYZ file of methanol with ...
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### Can specifications of a second-order phase transition of a solid be obtained with the Hartree-Fock (or DFT) calculation?

At some temperature a crystal lattice of a solid can be rearranged or to say it more precise - got new positions of its cores. This phenomenon is well-known to be called a second-order phase ...
• 601
43 views

### How to calculate the formation energy of a defect using the unit cell?

I want to dope CuI conventional unit cell using Quantum ESPRESSO. In previous papers they used different formulas of defect formation energies,and they use supercell. So I'm confused. What's the ...
• 855
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### Regarding SISL package of siesta

I want to visualise MPSH (molecular projected self-consistent Hamiltonian) orbitals using SISL package of siesta, is there any manual or guide for it. I have searched in internet but didn't get any ...
• 307
32 views

### External magnetic field in magnetic shielding calculations

There is this method called nucleus-independent chemical shift (NICS) to calculate the magnetic shielding values at different spatial coordinates of a molecular system. It can be used to estimate the ...
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15 views

### Issue with getting pw_bands output file for ws2

After running the input pw_bands.in file execution is not stopping even after 10hrs , and the output is not updating anything further after 1 min of the output.