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Questions related to Atoms
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 2,692 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 6,941 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 6,010 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 6,338 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 2,813 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 2,208 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 8,023 0 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 3,466 1 View
Could someone help me, I have a cif file and I want to perform electronic structure calculations in abinit or qe, however, when viewing the cif file, it presents several identical structures...
22 February 2022 1,556 3 View
Hello, I am trying to fit the atom. I tried to match PEG to density, because my crystallization condition contains PEG. But I can see the appearance of negative density after refinement. What...
22 February 2022 1,271 3 View
Hello, Can anyone recommend a tool for measuring the orientation angle between two domains of a protein? Thanks
22 February 2022 4,431 3 View
Dear all, Im looking for a tool that would help me find the binding sites of a given set of TFs, I have tried Ciider but wasn't able to get it working on my machine.
21 February 2022 143 3 View
----- Orbital basis set information ----- Your calculation utilizes the basis: def2-SVP F. Weigend and R. Ahlrichs, Phys. Chem. Chem. Phys. 7, 3297 (2005). ----- AuxJ basis set information...
18 February 2022 1,554 2 View
Hello Researchers! I encountered a system for XRD crystal structure refinement using FullProf Suite, where the one unit cell contains 4 formula units and a total of 30 atoms. For refinement I...
15 February 2022 5,704 2 View
I have taken a protein and because of its larger size I have taken the residues around the active center. Because of this, there are missing residues and the residues are not in chain. I want to...
10 February 2022 474 3 View
Hello everyone, I am trying to prepare a protein that I received which was refined. The issue is that when I try to prepare a topology file on GROMACS, I get the following error: Fatal...
10 February 2022 5,146 4 View
Dear Respected Members I want to calculate the FM and AFM ground state energy using interface of CASTEP. I build 2*2*2 supercell of ZnO (Hexagonal), containing 16 atoms Zn and 16 atoms O. Then I...
08 February 2022 1,019 1 View
I am trying to run a interaction studies between two molecule for Hydrogen abstraction (HAT mechanism). So when i put two molecules together in Gaussian at 3-21G basis set, the HAT is happening...
03 February 2022 2,118 3 View
Dear all, I tried to simulate SI nanoparticles with MD using spherical structures , I don't have the data file for clusters of 2922 atoms the file attached contain only 2654 atoms. could anyone...
02 February 2022 5,668 1 View
How can we calculate the defects in Crystal? Can anyone suggest the formula to measure the defects from XRD data?
02 February 2022 9,642 5 View
I am not sure how much NBANDS should I consider while doing the optical calculation in VASP. Cam anyone please explain here how much one should consider. Thanks, Poonam S.
02 February 2022 644 2 View
A sample of water and xerogel was prepared and used. The sample was put in the NMR machine. Then, the sample was inserted in the dryer and then again in the NMR machine several times. The same...
02 February 2022 3,970 3 View
Dear all, I am studying electronic structure of quantum dots using castep. And I would like to passivate the dangling bonds with hydrogen atoms, but as mentioned in the attached papers,there are...
01 February 2022 6,250 3 View
Hello everyone, I am not able to do structural optimization of a nanotube with 46 atoms on multicore. Is there any suggestion to get rid of this. Also what are the restriction on atoms during...
31 January 2022 2,729 3 View