Questions tagged [reproducing-data-from-papers]
When there's a calculation or data in a paper that the user is trying to reproduce.
11
questions
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votes
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Creating Monoclinic boxes with Packmol?
I am trying to reproduce this paper and the unit cell for the system is Monoclinic. I have already generated the surface, and now need to generate the waterbox that is placed in contact with the ...
- 2,762
2
votes
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How to set G-type AFM and U parameters in VASP when optimizing structure?
I am trying to reproduce results from research. In computation details part, it mentioned some setting about G-type AFM and Hubbard parameter:
1.
A Hubbard parameter (U) of 5 eV was used to treat the ...
- 395
2
votes
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answers
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Thermal conductivity of cylindrical Si nanowire is lower than expected
I am trying to recreate the results from this paper. Specifically, the nanowire I am testing is cylindrical with a cross-sectional area of 24 nm2 and a length of 10 nm. I am expecting a thermal ...
3
votes
1
answer
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Visualising the spatial distribution of water structure using VMD
I am trying to recreate Fig. 5b of this paper
I have a solvated NH4+ in my system and would like to create a similar visualisation for my case.
Can this be generated using VMD? If so could someone ...
2
votes
0
answers
43
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How to calculate the polarization caused by doping induced lattice distortion? [closed]
In this paper "Lattice distortion induced internal electric field in TiO2 photoelectrode for efficient charge separation and transfer", the authors calculated the polarization of anatase ...
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2
votes
0
answers
139
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How to include the spin-orbit coupling strength of only two or three elements in VASP? [closed]
I am trying to calculate magnetic properties in my material with VASP, much like Fig 3b of this paper. The paper says:
"To understand the origin of the SIAin monolayer MnBi2Te4, we performed the ...
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3
votes
0
answers
131
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Problems with Lennard Jones potential parameters reading [closed]
So I was given this link, and was happy that I have now the epsilons and sigmas that I can use in Lennard-Jones potential calculations, but found out that the information in other sources is very ...
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11
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140
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How to solve general wave equation and dispersion relation using Fourier series? [closed]
In this paper (open access), the authors used Fourier series with most general wave equation to find the dispersion relation. I am presenting some main equations as snippets to depict their solution. ...
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10
votes
1
answer
146
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Understanding the rigorous bridge between atomistic and coarse-grained simulations
I am currently reading this paper by Noid et. al. on the rigorous bridge between atomistic and coarse-grained simulations.
In the paper, he defined a linear map from the atomistic coordinates and ...
- 4,141
11
votes
1
answer
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Unable to recreate data for benzene from paper in GROMACS 2020.5
I have been trying to simulate benzene in OPLSS-AA forcefield as per this paper: https://pubs.acs.org/doi/10.1021/ct2002122. I have been at a loss, since I believe I have everything running as per the ...
- 4,141
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Inconsistent data of chemical potential from different papers [closed]
I am looking for chemical potential from literature.$^{1,2}$
I compared the method and data they provided. They use the Fitted Elemental Reference Energy method via GGA+U on VASP employing PAW. The U ...
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