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I'm currently working with fingerprints calculation in molecular dynamics trajectories.
To do this I need to convert protein and ligand in a pdb file for every single frame, and then reopen every fil…
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Trajectories should be a simple extension of the structure API (see Issue #23)
Suggestion :
`lattice_vectors_trajectory` : list of each lattice_vectors-like (as defined in structure, see Issue #…
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Opened issue to list here other Python libraries to be checked.
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I would like to know it the specification allows to export a scene that contains topology and trajectory from two different resources?
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Instead of implementing ES logic externally we prefer to use GROMACS to do this. This should reduce bugginess, instability and complexity.
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Hello,
I came across the paper [1] and found this code. In the paper, the diffusion coefficient is extended to infinite lag time. I have doubts about it.
If I understand the theory correctly, th…
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Hi everyone,
I'm getting this error (ValueError: unitcell angle < 0) when saving trajectories.
It happens with different trajectory formats and it is quite random since sometimes it happens and so…
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Dear Molly developers,
I have been working on ion implantation simulation for a while and want to develop some new algorithms to deal with the microscopic collisions. Then I came across `Molly.jl`,…
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## Is your feature request related to a problem? ##
I am doing molecular dynamics simulations in VASP and would like to use MDAnalysis to analyze the trajectories.
## Describe the solution y…
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Speaking personally, the best outcome of this would be to find that someone has already solved the problems we're thinking about, or at least at least has a solution that can be extended to cover this…