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Questions related to Atoms
I am using CASSCF method by qchem software. So, i am facing difficulty in how to choose active orbitals and active electrons for a molecule and also i am also confused about the step wise...
29 May 2022 3,785 2 View
I need the POSCAR file .
25 May 2022 5,977 0 View
I would build CoMFA and CoMSIA models, can we use 16 molecules as datat set of 3D-QSAR?Thanks for your answers?
19 May 2022 9,439 4 View
I have used QwikMD/NAMD to run a simulation of a system containing two protein chains, and I would like to calculate the free energy of the binding interaction. How would I go about doing this?...
03 May 2022 4,227 4 View
Hi, and Assalam alikum, I want to prepare .mol2 file of Pd(II) complex for docking through Swissdock. Whenever, I upload the file it gives an error. I tried to prepare the .mol2 file via gview,...
20 April 2022 5,669 0 View
I am looking for a technical guide for ultrasonic homogenizer design and manufacture. I need a detailed explanation about how to design a transducer, booster and horn system for homogenizing...
20 April 2022 1,008 6 View
I would like to know the convenient ways by which we can dissolve the decellularised cell-derived matrix (CDM) and this same CDM solution we can use to form gel again after some period of...
06 April 2022 7,553 0 View
Tin whiskers are a well known phenomena in the electronics industry which, while known about, do not appear to be very well understood. While they form on tin plated surfaces and can grow to...
02 April 2022 2,034 1 View
Dear All, I docked a ligand using Autodock vina and performed MD simulations for about 100ns. I need help in analysis of the results. If we see the results can we say the ligand detached from...
01 April 2022 1,464 3 View
hello dear friends How to find Lennard-Jones parameters for a particular atom? I find Lennard-Jones parameters for Mg-Mg , Si-Si, Mg-Si, Al-Mg, Al-Si thank you
31 March 2022 5,913 3 View
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 3,662 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 1,084 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 6,314 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 648 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 8,904 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 3,466 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 8,996 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 3,065 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 3,678 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 8,267 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 570 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 6,545 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 7,401 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 7,083 3 View