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6 votes
Accepted

Understanding the rigorous bridge between atomistic and coarse-grained simulations

Before working through the equations, I'll try to explain the logic behind what they are doing. It helps to think of think of their process backwards and assume they want an expression like equation ...
Tyberius's user avatar
  • 15.6k
5 votes
Accepted

Unable to recreate data for benzene from paper in GROMACS 2020.5

Thanks to the generous time and comments of @ShoubhikRMaiti, I was able to recreate the simulation. The problem in my code was 2-fold: I was using the topology filed created by LigParGen, which had ...
megamence's user avatar
  • 4,171
4 votes

Band gap do not match to published result in DFT using BURAI GUI of Quantum Espresso

Since you used BURAI, it's safe to assume that you used either an LDA or a GGA functional for your pseudopotentials (PP). In order to confirm, check if you have pz or pbe in the name of your PP. It ...
Abdul Muhaymin -Free Palestine's user avatar
3 votes

Why does the C6z operator have 6 eigenvectors in this paper?

The paper appears to have an error. When a $C_6$ operator acts on an atom's (x,y,z) coordinates, the operator's matrix representation is the 3x3 matrix that you correctly provided in your question ...
Nike Dattani - No Free Time's user avatar
3 votes
Accepted

Visualising the spatial distribution of water structure using VMD

The figure that you have provided depicts the spatial distribution of water molecules around the NH$_4$$^+$ ion. This is generally generated by calculating the 3D probability density of water-O atoms ...
Hemanth Haridas's user avatar
1 vote

Visualising the spatial distribution of water structure using VMD

VIAMD software will allow you to do that. You can use the sdf function in the script editor after loading your trajectory. It would like something like that depending on your topology: ...
mathieu linares's user avatar

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