Questions tagged [reproducing-data-from-papers]

When there's a calculation or data in a paper that the user is trying to reproduce.

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12 votes
0 answers
171 views

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 ...
Binh Thien's user avatar
  • 2,025
11 votes
1 answer
303 views

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 ...
megamence's user avatar
  • 4,141
11 votes
0 answers
137 views

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. ...
Siddhant Singh's user avatar
10 votes
1 answer
141 views

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 ...
megamence's user avatar
  • 4,141
3 votes
1 answer
98 views

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 ...
Priyanshu Gupta's user avatar
3 votes
0 answers
114 views

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 ...
John T's user avatar
  • 564
2 votes
0 answers
18 views

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 ...
Tieyuan Bian's user avatar
2 votes
0 answers
31 views

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 ...
wienerwastaken's user avatar
2 votes
0 answers
121 views

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 ...
liao guo's user avatar
1 vote
0 answers
35 views

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 ...
Hemanth Haridas's user avatar
1 vote
0 answers
36 views

How to calculate the polarization caused by doping induced lattice distortion?

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 ...
meTchaikovsky's user avatar