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Questions related to Atoms
I tried to do homology modelling using MODELLER and I calculate the RMSD value of the template structure and the model result using PyMol. The result shows...
25 September 2021 3,386 3 View
Hello Everyone, Iam trying to do the spin polarisation calculation using quantum espresso. I tested BCC - Fe and it works by adding nspin=2, starting_magnetisation=0.5 But for the material...
21 September 2021 5,247 4 View
I know basic definition of grain boundary and phase boundary. However, can we consider grain boundary as phase boundary as crystal orientation is different?
20 September 2021 1,757 5 View
Using the pdb2gmx module, I separately parameterized two proteins (polymers), I used the topologies of both and joined them in a single topol.top file. I have minimized the energy and the gromacs...
16 September 2021 9,760 1 View
Parameterizing proteins with CHARMM36 and getting the error "WARNING: There are no atom pairs for dispersion correction" when running a simulation in GROMACS 2020. Using the pdb2gmx module, I...
16 September 2021 9,904 2 View
Greetings everyone, I have a question regarding the effective mass tensor, that I cannot seem to find the solution for: I have used DFT to calculate the bands/eigenvalues of Silicon. I have done...
14 September 2021 9,001 3 View
I am using this following code babel -i sdf *.sdf -o pdb > *.pdb --gen3D I got warnings like 3D coordinate generation failed Errors/Warnings *** Open Babel Warning in CorrectStereoAtoms...
09 September 2021 6,706 4 View
I was trying to add hydrogens to my protein to prepare it for docking when it said that there are non bonded atoms and when I tried adding hydrogens anyway, an error appeared saying 'IndexError:...
09 September 2021 10,015 1 View
Coordination chemistry.
09 September 2021 267 3 View
This is the part of the input script. While running the simulation an error is showing ERROR: Kspace style requires atom attribute q (src/KSPACE/pppm.cpp:208) # vibration analysis simulation units...
08 September 2021 479 1 View
Thank you for your help in advance.
06 September 2021 7,268 2 View
I have incorporated a single impurity in 1*5*1 supercell of GaN. For 4 different atoms from group IV I have found the same lattice constant. Is it normal?
04 September 2021 4,350 3 View
Since graphene has metallic bandgap, incorporation of carbon atoms should reduce the energy bandgap of the host material. Can the opposite behavior be found?
01 September 2021 7,018 3 View
Being is a function that can be found by using only one in all of the units of time (past, present and future). An object essentially has a dimensioning according to time. The size of an object is...
31 August 2021 6,242 3 View
For obtaining gamma phase, previously ball milling was done fpr a short time and then laser cladded. Just for trial and error. However, the desired phase was not reached.
28 August 2021 199 2 View
Dear all, To get the magnetism in the nonmagnetic host material, I would like to know how much percentage doping we can do. Is there any minimum or maximum doping percentage defined or it is...
26 August 2021 9,559 3 View
Hello, I am trying to view the interactions between a ligand and a protein after a 1000 ns molecular dynamics simulation with GROMACS. I have done this before with the same ligand and many other...
25 August 2021 9,753 2 View
C=(nNAe)/3.6M this is the formula for Energy storage capacity of Anode. where n is number of metal atoms adsorbed per mole of doped graphene [how this will be calculated]? Na- Avogadro's...
23 August 2021 4,097 1 View
the absorption of carbon quantum dot by hydrotermal method at 180 c higest than 240 c why ?
22 August 2021 6,848 4 View
The code that I wrote is as follows: 1 clear 2 units metal 3 dimension 3 4 boundary p p p 5 atom_style atomic 6 lattice fcc 4.05 orient x 1 1 -2 orient y -1 1 0 orient z 1 1 1 7...
21 August 2021 339 2 View
I have tried to change various parameters, but once I add an electric field(3eV) the system cannot be converged. The system includes: Graphine, BF4, BMIM, CO2 Condition: Applied External...
21 August 2021 6,917 3 View
Hello, I am trying to calculate interaction energies of ligand with a protein that I got from ACEMD simulation (I have the file has a .psf file) and I intend doing that using the below script;...
17 August 2021 554 2 View
I am currently running some QTAIM topology analyses of main group compounds to elucidate their electronic structures. In particular I would like to use delocalisation indices (DI) to quantify...
17 August 2021 5,059 3 View
My experiment needs to consume ~400mg catalyst every time, but it takes three days to synthesize 1g, and it also needs tableting and sieving. At present, the focus of the experiment is not the...
09 August 2021 2,003 7 View