Atoms

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Is it acceptable to use different values of Hubbard's U potential for applications in zeolites?

I have used the linear responce method to calculate Hubbard's U in VASP as indicated by VASP tutorals in their website. I give the...

09 November 2021 558 8 View

How to compute H2O -- Cl- hydrogen bonds with gmx hbond?

Hi, I'm simulating a box with water and Li+ and Cl- ions and I'm trying to calculate the hydrogen bonds formed by the Cl- anion and the water molecules using the gmx hbond. The command I was using...

08 November 2021 5,622 3 View

How we can calculate the interaction energy at a certain critical point (CP) in QTAIM (Atoms in Molecules)?

I want to calculate CH-pi, H bonds, and other kinds of interactions separately in a crystal structure using QTAIM analysis. Is there any guide for doing this? what parameter should be...

04 November 2021 7,553 3 View

Band structure and PDOS mismatch?

Please I have solved that issue but I have another problem. I doped a supercell and after performing spin-polarized calculations the spin-up bands show a metallic structure whereas the spin-down...

02 November 2021 737 9 View

What are the All-Atom parameters for methanol in the Kirkwood Buff force field?

In the the following paper, they mention the use of methanol in the Kirkwood-Buff forcefield Computational Calorimetry of PNIPAM Cononsolvency in Water/M... However, when I go to the article...

01 November 2021 6,708 3 View

P-type conductance from Te doping in GaAs?

Group-IV elements doping in III-V behaves amphoteric: n-type if the dopants occupy the group-III sites and p-type if they occupy the group-V sites, which is not hard to understand. My question is...

31 October 2021 436 3 View

How can I synthesize ZnO nanorods of very homogeneous size?

For a catalytic process, I need to synthesize very homogeneous ZnO nanorods, no more than 100 nm in length. Could anyone suggest some effective method? Until now, the synthesis has been carried...

28 October 2021 8,272 8 View

How can I generate lots of ghost atoms above the muti-ring molecule to get the value of NICS-zz ?

Hello everyone~ I'm trying to calculate the NICS-zz Scan, and I want placing Bq atoms in line and above the molecule plane. How can I generate lots of ghost atoms above the multi-ring molecule to...

27 October 2021 3,419 2 View

Autodock docking error, how to solve the problem of protein can not be converted to PDBQT format?

I would like to ask all the teachers. When Autodock was docking, I added hydrogenation atoms, removed water, and grid selected protein, but there was an error. warning： -contains no non-bonded...

23 October 2021 7,193 2 View

Can lammps output the equilibrium position of the atom or internal atomic coordinateof single crystal primitive cell?

As we all know, VASP or other DFT calculation can give equilibrium position of the atom easily after optimization. However, if you use lammps, we should use supercell. Can lammps output the...

23 October 2021 5,844 2 View

How to save my pdbqt file with desired pose for the ligand-protein complex, AutoDock is not saving a particular one, instead saving all?

I have performed molecular docking and found 9th conformation is the best for me as it has the minimum amount of binding energy. Now I want to save it for using later analysis in BioVia Discovery...

18 October 2021 7,393 5 View

Can anyone help me solve this problem with Powdercell ? I can't illustrate the second atom on the image?

I used Powdercell to draw the ZnO_hexagonal crystal structure but when I finished entering the data, my O atom did not appear on the drawing, I checked the data table again, the O atom did not...

14 October 2021 4,411 3 View

How the hard features develop in a variety of coatings/thin films synthesized by different vapor deposition techniques?

What are the key elements developing the property of hardness in materials synthesized by the different compositions of solid and gaseous atoms? (Please check the link of article...

13 October 2021 5,918 3 View

Can we use VASP to compute Dipole moment of a solid using VASP?

I used IDIPOL=4 tag to compute the dipole moments along each direction of a hybrid perovskite. It has 96 atom. I first did geometry optimization with PBE and compute the dip moments on the relaxed...

13 October 2021 5,161 3 View

How do I add Molibdenum atom in autodock databse and have Vina to read it during automatick docking?

I would like to automatically dock 150 molecules using Vina, but after setting up everything I get the error: "Parse error on line 11572 in file "protein.pdbqt": ATOM syntax incorrect: "Mo" is not...

11 October 2021 9,278 3 View

How can I join files of several trajectories of the same molecule to make an analysis?

I had to extend my GROMACS simulation four times and it finally gave me four trajectories, I was able to merge all four with gmx trjcat, however, it still comes out: Fatal error: Molecule in...

08 October 2021 9,612 1 View

What is the way forward about Machining Atomistic modelling?

I am PhD research student at a university in Scotland. I am in my first year with background in Materials and Metallurgy. I want to go into simulation particularly MD. My proposal research is on...

08 October 2021 348 2 View

How to create gas molecule-surface adsorption model for gas-sensing in BURAI??

I added a gas molecule over the surface of my slab model using the "Put an atom" feature given in BURAI 1.3. However, when I tried running the vc-relax for this structure in quantum espresso, it...

07 October 2021 8,748 2 View

How to calculate ionization spectra(core orbital spectra i.e. x-ray spectra) using Gaussian09 or Oraca?

I want to plot ionization spectra for Singly, doubly, and triply ionized molecule i.e. to be more specific is the x-ray spectra for singly to triply ionized atom or molecule using Gaussian or Orca ?

05 October 2021 4,699 3 View

Why is the solution of quantum harmonic oscillator not possible within old quantum theory?

Eigen energies of Hydrogen atom, treated as a central force problem, can be derived with Bohr model. Given the basic nature of the harmonic oscillator problem, it is a bit surprising why its...

30 September 2021 7,775 7 View

How can I use different basis set for different atoms of same molecule in an ORCA input file. What additional keyword should I use?

I want to use TZVP for Ni and 6-311G* for C, H, and O present in the molecule.

29 September 2021 2,459 2 View

Can anyone tell me that where can I find the atom symmetry codes for a crystal structure?

I have crystal structure of a newly synthesized metal-organic framework. I want to know the atom symmetry codes of the asymmetric unit of the crystal. Please help me. Thank you in advance.

29 September 2021 8,020 3 View

Do I need to mention the charge infornt of the atom while specifying different basis set for different atoms in a complex if "gen" keyword is used?

I have Cu, C, H, O, N in a complex, and +1 charge on the complex. I am interested in using LANL2DZ basis set for Cu and 6-31G(d,p) basis set for all the other atoms. can someone please suggest me...

28 September 2021 8,992 3 View

Is it possible to model only certain atom in the modeller using Model-ligand.py?

I have a generated a model based on a template. this template also contains a natural ligand, 4 calcium atoms, and a zinc. I would like to add the zinc and calcium atom but not the natural ligand....

26 September 2021 5,539 1 View

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