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Questions related to Computational Chemistry
I am using BURAI 1.3 as GUI for Quantum Espresso. If I save the project in BURAI, it creates several .in files. Can I run these files using the Terminal? Do I have to follow any specific order?
08 February 2020 9,213 4 View
I am working on a project regarding gas sensors using nanoparticles. Is there any software that I can use to computationally analyze the gas sensing abilities of different metals/materials?
05 February 2020 866 3 View
Hello, I am doing DFT simulations for various organic molecules using Gaussian 09 software. But some dyes are not getting optimized (showing error in the output file). Moreover, I want to obtain...
03 February 2020 5,593 8 View
NBO analysis of a donor-acceptor interaction not showing any NBO associated with that particular interaction. Although there are no NBOs associated with the interaction we are interested in, is it...
01 February 2020 6,520 5 View
Hi, I am working on an organic pesticide molecule, thiram. For DFT calculations, I have constructed a thiram molecule in GaussView 5.0.8 and submitted my job to Gaussian 09 working in Tyrone...
29 January 2020 2,171 4 View
Hello everyone, I'm doing some QSAR analysis with a data set which contains some coordination complexes. In order to incorporate some chemical knowledge into the descriptor set I'm going to use...
14 January 2020 7,177 4 View
Hi, I'm up against a horrible deadline so I'm hoping for some help figuring out what I'm doing wrong. I have a list of custom atom names in Gromacs of which I want to perform hydrogen bond...
11 January 2020 7,705 6 View
For virtual screening, what area of the receptor should be selected as the search box for the binding site, if the area around the bound ligand in the pdb is far away from the catalytic triad in...
07 January 2020 7,591 3 View
In gaussian when I do the 《fopt freq M052X/6-311G(d,p)》analysis and some other times with another method and basis sets I face to notice (no special actions if energy rises). What should I do?
15 December 2019 1,573 3 View
I am trying to find a transition state using QST2 with b3lyp, but I am getting the following error: "New curvilinear step not converged. ***** Convergence failure in GTrans ***** Try using 3...
12 December 2019 4,952 2 View
Has anyone already performed DFT calculations for cellulose and functionalized cellulose monomers? How can we do it to calculate the bond dissociation enthalpies and IR frequencies?
24 November 2019 2,819 3 View
Hello, I am new to NEB and have been trying to plot the diffusion of Li across various TMD monolayers. For some of my activation energy plots, I get small peaks. I believe these are due to some...
22 November 2019 4,611 2 View
I want to calculate charge transfer integral to transfer one charge from one part of the molecule to another part. what are the proper ways to calculate this? And which software package is good to...
13 November 2019 6,806 3 View
I am doing calculation to see excited state and ground state raman intensities. I have successfully done it for ground state using dft and after finding absorption wavelength , have optimized the...
09 November 2019 8,121 3 View
What is the best method (in HF/DFT/CDFT) to calculate the off-diagonal coupling elements H_12 for electron/hole transfer in a molecule (intra-molecular electron/hole transfer) ? I have used...
23 October 2019 7,248 5 View
Is there any method based on Koopman's theorem to calculate the off-diagonal coupling elements H_12 for electron/hole transfer in a molecule (intra-molecular electron/hole transfer)
22 October 2019 2,909 9 View
Using TURBOMOLE, I am studying a mechanism of Heterolytic vs Homolytic cleavage. When the bond breaks, there are three possibilities a) Heterolytic Cleavage (RHF, singlet) b) Homolytic Cleavage...
16 October 2019 4,758 5 View
I am using AMBER for MD. However I am not able to figure out how to select atoms or residues to apply a harmonic restraint. I have crystal structure from PDB and and I want run MD simulations on...
09 October 2019 3,020 3 View
Hi everyone, I’m pretty new to the world of data based Research, but as I explore deeper, I’m realising that I’m producing a lot of files that are becoming hard to track. I have a background in IT...
08 October 2019 3,867 3 View
I am fairly new at using this software and at computational chemistry in general. I achieved what is believed to be a good TS before running the IRC but we are repeatedly receiving the same "bad...
23 July 2019 9,731 1 View
Does anyone know of a free program to calculate ESP? MOLDEN seems to be only for academic use, GaussView requires purchasing a license, are there any other sources? I have been using IQmol...
07 July 2018 7,931 6 View
I am trying to model systems with hydrogen bonding interactions of heavy in which the acceptor is an ion like chloride or bromide. Which level of theory, among B3LYP-D3 and MP2, will be better for...
24 May 2018 4,268 6 View
I am beginner of computational chemistry. I want to find out the reaction mechanism of formaldehyde with ammonia so please help me.
12 May 2018 2,724 5 View
How would you recommend using semi-emperical method for a TS search and property calculation including verification of the TS using ab intio method?
28 April 2018 4,961 5 View