Unanswered Questions
44 questions with no upvoted or accepted answers
22
votes
0
answers
248
views
Is there a software that can do derivatives with respect to user defined vibrational modes?
I'm doing some property calculations that depend on a sum of derivatives of some quantity with respect to normal vibrational modes. I was hoping to find some physical intuition relating the type of ...
- 15.9k
6
votes
0
answers
105
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What are the parameters in PySCF's Selected Configuration Interaction code
Dear StackExchange Members,
I'm using the native PySCF implementation of selected configuration interaction (SCI). However, I can't seem to find any documentation detailing the algorithm or various ...
- 20.1k
6
votes
0
answers
77
views
Benchmarking DFT vs Experimental Gaps - Confusion over Fundamental and Optical Gaps
Recently, I've come across discussions about the differences between fundamental (or electronic) bandgaps and optical bandgaps, with the two quantities differing mainly by the electron-hole binding ...
- 1,366
5
votes
0
answers
41
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Rich editing of ASE images
I want to produce some images related to graphene-like materials.
I was able to draw them using ASE visualize module after constructing the atomistic model. However ...
- 24.2k
5
votes
0
answers
162
views
Actual calculation of Coulomb energy in DFT softwares
I have a question about the actual calculation of classical Coulomb interaction term in density functional theory (DFT) softwares.
Of course I understand the form Coulomb energy as:
$\int\int \frac{\...
- 1,799
4
votes
0
answers
44
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What software is fit for calculating an atomic and electronic structure of a newly formed nanocluster after injecting impurities into an initial one?
Let's suppose there is a nanocluster and its structrure is known. The problem is to inject impurities into this nanocluster. The impurities can be injected in different quantitites but consist only of ...
- 1,027
4
votes
1
answer
141
views
How to use rigid scan with dummy atoms in gaussian?
I am trying to use rigid scan using gaussian 09. In my case, there are three water molecules and I have placed a dummy atom at the centroid of the three water molecules. For simplicity, I want to ...
CommunityBot
- 1
4
votes
0
answers
77
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Solvation_analysis subpackage for MDAnalysis multi-atom solute
I have a simulation trajectory from DFTB+ for 1 NaNO3 in 32 H2O molecules. The trajectory is in xyz format and I converted a frame of xyz to pdb using openbabel to serve as topology input.
I am ...
4
votes
0
answers
46
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Which one of the following showing the correct structure Jsmol or Vesta? Or they are just same
Let me explain. I found that the structure for TiFeSi given in the ICSD database using Jsmol software is a little different from what can be obtained using Vesta software using the same cif file ...
3
votes
0
answers
18
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NaN result using ShengBTE
I tried using ShengBTE t get the thermal conductivity of PE after performing phonon calculations using quantum espresso. When I used version 1.5.0 ShengBTE I got some numbers at the beginning of the ...
- 31
3
votes
0
answers
36
views
How to correctly set the high-symmetry point path block when there are breakpoints in the recommended path?
I watched Dr. Mohan's tutorial video, and the settings he provided are as follows:
...
- 31
3
votes
0
answers
50
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How can I restart a job in VASP software?
I'm running an AIMD (Ab initio molecular dynamics) calculation in the NVE ensemble with a specific initial kinetic energy (without using temperature control). My job stopped before the simulation time ...
- 617
3
votes
0
answers
31
views
martinize issue
PS C:\Users\MALINE\Desktop\martini> python martinize.py -f polypropylene.pdb -o output.pdb
...
3
votes
0
answers
62
views
Adding a molecule in AMBER
I'm new to computational chemistry. I want to model the enzyme EGFR and a small molecule Lapatinib. I got a .pdb file of EGFR at the Alphafold website, and got a .sdf file of Lapatinib at the pdb site....
Leo
3
votes
0
answers
57
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How to compute molar Gibbs free energy (chemical potential) for single molecule using gaussian09?
I want to calculate the Gibbs free energy of single gas molecule (AsH3) using Gaussian 09, but I am confused between "Thermal correction to Gibbs Free Energy" and "Sum of electronic and ...
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