Unanswered Questions
21 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
5
votes
0
answers
41
views
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
163
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
142
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
views
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
views
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
19
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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
51
views
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
77
views
Electronic density of states from not the usual VASP outputs
In a very frustrating development, my VASP has decided to hang at the writing of outputs stage. While I troubleshoot that separately, for the moment I need to get an electronic density of states from ...
- 1,658
3
votes
0
answers
84
views
How to generate pole figures from limited amounts of area detector X-ray diffraction from thin films (explain it like I'm five years old)
Historically powder X-ray diffraction was the go-to method for reconstructing crystal structure. X-ray sources were limited in intensity and emittance and so to collect data in a reasonable amount of ...
- 2,074
2
votes
0
answers
75
views
Spontaneous polarization of WSe2 using VASP
I am trying to use VASP to calculate spontaneous electric polarization in WSe₂ (semiconductor) with the following INCAR settings:
...
- 86
2
votes
0
answers
35
views
Are there any good tutorials on SHARC-Gaussian interface?
I am an aspiring quantum chemist planning on trying out the SHARC approach to study excited state proton transfer dynamics of organic molecules. I am comfortable with Gaussian 16 as that is the ...