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Hi,
When I try to visualize the trajectory with pymol, I see that the ligand and protein are in different parts of the water box (due to the periodic boundary conditions) and this is making hard to…
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Seems like a leftover relic from a time when we only had 1 pressure solver for `(Periodic, Periodic, Bounded)`.
Might be good to be explicit about the topology, but maybe we should wait until all …
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From @snilsn:
A theoretical case:
Imagine 3 features with increasing threshold values. Feature 1 + Feature 2 and Feature 2 + Feature 3 are closer than the minimum distance, but Feature 1 + Featur…
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When I run the asv_wave_sim and the boat reaches the end of the water surface it just keeps on floating in air. Is there a way to have the entire map be water and when it reaches the end it just loops…
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Hi, I am using CellListMap to apply a couple of functions to a catalog of ~16M objects. The general idea is as follows:
```julia
using Random
using CellListMap
mutable struct Catalog{T}
pos::…
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Greetings
I write to you because I am trying to run a MD of a Protein that interacts with a strain of RNA, but somehow the protein and the strain in the PDB are perfectly centered, but as soon as I …
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While debugging a student code I found out the following behavior which looks like a bug to me. If one initializes the system with particles in different periodic images (for example some inside the s…
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[https://drive.google.com/file/d/1lX3K406KrUcl--BUASQ1JSNxHRKvMPz8/view?usp=sharing](url)
Excuse me, I am new in using molecular dynamics softwares, and I was trying to figure out how it works on m…
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I noticed that `similar(::Field)` does not transfer boundary conditions
https://github.com/CliMA/Oceananigans.jl/blob/a86ef32581192d82a655e1b2ff4411e79917a379/src/Fields/field.jl#L217-L227
so we…
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Hi, I am using the delaunayn function in this package, and since I am working on structure graphs of crystals its important that the delaunay traingulation be performed on my system considering the pe…