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Questions related to Atoms
Hello all.. My question is regarding the size of a supercell for doping studies through DFT calculations.. Actually, I am dealing with a mono-layer and wish to see the effect of doping. For...
08 August 2021 8,192 5 View
Please help me to section and merge of group, i am new user and little confused which number i have to choose? Our Bi-layer model comprises of POPG/POPE. (Generted from Membrane builed) Version-...
07 August 2021 8,908 1 View
Hi, I am trying to study the charge transfer of certain molecules to understand the sensing properties. I have calculated the Mulliken population using Quantum ATK tools. Now how can I understand...
06 August 2021 683 2 View
In general, if the molecular structure is given, then how can we calculate the distance between two atoms. I need to know the distance between Zn-Zn atoms in ZnO and Zn3N2 molecules, I also need...
04 August 2021 9,829 5 View
I am using Gaussian to perform excited-state calculations on a coumarin derivative. In the input file, I have drawn the molecule correctly. The output files always come out with altered bonds...
02 August 2021 6,743 3 View
Dear All, I need to compute the bond strength between two atoms, in a molecule with 20 different atoms. I already have the relaxed structure from DFT and the forces acting on each atom, but I...
29 July 2021 9,999 3 View
Got this error while performing docking in Pyrx after running vina. ligands and proteins both are optimized can someone help??
26 July 2021 6,463 4 View
I am trying to do dft calculations on the surface of Heterogeneous catalysts using Quantum espresso code. What would be a good software (free or open-source if available or other paid options) to...
21 July 2021 2,749 5 View
Can anyone please explain which type of structure is preferred for a ligand-Receptor docking study? When both the NMR based and X ray crystallography based structures both are available in PDB?
14 July 2021 6,801 7 View
Curie Temperature using ab initio technique; basically computational way
10 July 2021 7,572 6 View
I have a 20a x 17a x 20a simulation box filled with bcc tungsten atoms. What lammps command can I write to make 20a x 2.5a x 20a at the bottom of the box "immobile"? The script below shows how my...
08 July 2021 4,270 6 View
I am trying to optimize the geometry of my ceria-zirconia mixed support to calculate oxygen vacancy formation energy using the CASTEP module in the Material studio. I am getting messages like,...
19 June 2021 7,196 6 View
I am performing an Unrestrticted Kohn Sham (UKS) DFT simulations using cp2k In my system of 289 atoms, I have 1 Fe atom. I would like to perform the DFT calculations for different spin states of...
10 June 2021 3,809 3 View
Thin Tin powder is widely used in solder and i believe most of it is produced by gas atomization. However i saw it claimed that available solder were all bigger than 10 micron particle and that...
04 June 2021 8,474 1 View
Hello everyone. I have two input files for reactant and product states of the same material. The atoms are to be arranged in the same order for both the states. However, the order of atoms in the...
19 May 2021 2,692 2 View
How to modify gold nanoparticles by thiol? GNPs are prepared with sodium citrate reduction and dispersed in water.
15 May 2021 358 3 View
After doing the Bader charge analysis, using below summed CHGCAR file, chgsum.pl AECCAR0 AECCAR2 bader CHGCAR -ref CHGCAR_sum bader net charge on atoms is different, i.e no two atoms have the...
29 April 2021 5,738 2 View
Consist of aluminium and zinc as major alloying elements.
27 April 2021 7,364 8 View
We are interested to prepare a setup for powder metallurgy studies. I'm trying to find a lab-scale machine or technology to produce good quality spherical metal powders of active metals like...
19 April 2021 5,433 3 View
I am simulating a gasification plant. I am getting this warning in the yield reactor. * WARNING THE FOLLOWING ELEMENTS ARE NOT IN ATOM BALANCE: C S H N I have checked multiple...
21 March 2021 7,710 2 View
Dear Researchers, I have synthesized two different compounds which is having a different number of atoms count, but similar type of atoms (i.e C, H, N, Ag). One structure is tetranuclear in...
18 March 2021 8,223 7 View
Hi, I am running MD simulations of a Gold-chelate compound with square planar geometry of Au (III). I parametrized the missing force field parameters for Au and its four neighboring atoms using...
14 March 2021 5,339 19 View
It is easy to perform calculations for compounds with known structures. But if we need to substitute other atoms reducing the content of one atom, it becomes hard for me to relax that structure....
12 March 2021 7,300 2 View
I am trying to bulid a dense aqueous Lysozyme sysytem by GROMACS. First, I creat a cubic box with side length of 8.7 nm. Then, I put several lysozyme molecules into the box with command...
11 March 2021 6,741 11 View