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Hello, I'm currently working on point defects, especially oxygen vacancies in YNiO3 and I use VASP. I first compute the ideal crystal, then I introduced an oxygen vacancy in a 3x3x3 supercell...
31 March 2022 3,731 3 View
Hi, all! I have recently used the AutoDockTools sofware. But it said that "added gasteiger charges found 44 aromatic carbons detected 0 rotatable bonds set TORSDOF to 0". And when I were doing the...
30 March 2022 1,160 2 View
I am searching for Transition States through VASP. I have Optimized all my initial and final states, but now I have a problem for finding TS. Is there any way to change the distance between...
30 March 2022 6,426 8 View
In output of CASTEP population calculation, there are Mulliken analysis and Hirshfeld analysis, both show values of spin of atoms. These values are not the same. So which one should we use to...
28 March 2022 720 3 View
In a QM/MM job, I got this error Include all MM classes Angle bend undefined between atoms 5983 5985 6621 OW-HW-HW [H,H,L] Angle bend undefined between atoms 5985 6621 6619...
24 March 2022 8,984 2 View
Dears, If there any open source (program) to plot the Nanopartciles and attach ligands. From such structure I would like to calculate the DFT? kind regards
24 March 2022 3,552 5 View
I am looking at a problem related to the Clausius-Mossotti equation. The Clausius-Mossotti equation is given by, chi = (4*pi*n*alpha)/ (1 - 4*pi*n*alpha/3) where, chi: susceptibility n: number...
22 March 2022 9,058 3 View
Hello everyone, My lammps input script is as following : units real variable cfac equal 1.01325e-4 variable cunits string GPa atom_style full boundary p p p pair_style lj/cut/coul/cut...
21 March 2022 3,263 2 View
I have a site disordered system, with multiple ions at particular site. I need to refine the occupancies maintaining the chemical formula and total occupany of 100% in fullprof. I tried giving...
19 March 2022 3,765 7 View
I am trying to perform a docking between my enzyme and the substrate using AutoDock Vina but the output of the program is a strucutre with atoms bond even when they are far, unnatural torsions......
16 March 2022 8,363 3 View
When i performed MD simulation with step: gmx solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro (define box 1.1 x 1.1 x 0.8),the results exhibited as: Generating solvent...
14 March 2022 640 4 View
Hello, I have been trying to obtain a single point using DLPNO-CCSD(T) but in some cases, I have obtained the following error: "ORCA finished by error termination in MDCI Calling Command: mpirun...
10 March 2022 6,621 1 View
Im looking for a multi sequence structural alignment tool that can align main chain atoms like main chain oxygen and main chain nitrogens in a PDB file. Or even better, one that specifically...
07 March 2022 7,478 2 View
Hello, I am modelling a polycrystalline CoCrNi medium-entropy alloy, into which I am trying to dope Aluminium atoms using MD simulations. I am trying to replace some of the CoCrNi atoms in the...
06 March 2022 7,156 3 View
Hello all Actually, I want to perform text classification using Bert algorithm on a text dataset that is imbalanced . I want to balance my data but first convert text to vector and then balance my...
04 March 2022 4,259 3 View
I have trouble understanding how to generate these files, because a pseudo potential is not necessary for the electron, and do I need to specify the electron in the POSCAR?
03 March 2022 2,763 2 View
I am running a DFT-D3 geometry optimization with ORCA5.0 of a condensed system (a portion of a pdb file; no metal ions). What I did? - I assumed it to be a closed-shell system but applied UKS...
03 March 2022 7,025 3 View
I need to assembly gold nanoparticles with calixarene. How dithiol molecules enter the cavity of cuproaromatics and bond with gold atoms.
27 February 2022 6,066 1 View
One of the most valuable properties that allows the 1H-NMR spectrum to give structural information is spin-spin coupling, which is caused by spin coupling between hydrogen nuclei that are not...
26 February 2022 6,420 4 View
I have a protein simulated. I want to measure the angle between two domains (domain II & IV) and use the third domain (domain III) as a hinge between them. First, I want to select center of...
25 February 2022 2,891 3 View
Hello all, I’m an undergraduate working on structure calculation for a protein – ligand complex for months but haven’t got any satisfying results so far. The following is my protocol and criteria...
24 February 2022 2,271 0 View
Hi All, I am using QE to do bader analysis. I Have generated the necessary files by using "http://theory.cm.utexas.edu/henkelman/code/bader/". But my question is this code gives bader charge file...
24 February 2022 8,084 0 View
What is a PSO algorithm (in optimization)? What are some examples of its applications? Thanks!
24 February 2022 5,238 3 View
I am sure that I am getting an underestimated bandgap in nanotube. But it is not feasible to do a Hybrid Functional calculation for such a large complex structure. How would anyone suggest me to...
22 February 2022 3,535 1 View