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Desmond trajectory reader #4268

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sperezconesa opened this issue Aug 29, 2023 · 4 comments · May be fixed by #4816
Open

Desmond trajectory reader #4268

sperezconesa opened this issue Aug 29, 2023 · 4 comments · May be fixed by #4816
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Component-Readers enhancement help wanted

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@sperezconesa
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Is your feature request related to a problem?

If I want to use MDAnalysis when I use desmond as the MD engine I have to convert it to some other format and then read that other format.

Describe the solution you'd like

For MDAnalysis to read desmond trajectories.

Describe alternatives you've considered

I convert to xtc with VMD and then read it with MDanalysis but this is inconvenient and a bit convoluted because using VMD as file converter is very inefficient.

Additional context

VMD has a desmond trajectory reader so perhaps that is a good starting place since it is open source.
@orbeckst
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Would be nice. Is there an official/public documentation of the format? That's usually the starting point.

We welcome contributions, especially for formats that aren't frequently used by the core developers.

@hmacdope
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CPPTraj seems to use the plugin from VMD: https://github.com/Amber-MD/cpptraj/pull/796/files shouldn't be too hard to wrap with Cython.

@IAlibay
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IAlibay commented Sep 4, 2023

CPPTraj seems to use the plugin from VMD: https://github.com/Amber-MD/cpptraj/pull/796/files shouldn't be too hard to wrap with Cython.

As long as it's just the DE Shaw files (which seem to be GPL compatible) that would be fine. We probably can't package anything from VMD though, at least unless the plugins are held under a different license.

@sperezconesa
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Desmond can output xtcs, the problem is the topology. DMS is not used by default anymore, it is CMS now as the topology. You might want to reach out to the Schrodinger people and see if they are interested in helping out.

@talagayev talagayev linked a pull request Dec 3, 2024 that will close this issue
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Implementation of CMSParser talagayev/mdanalysis
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@orbeckst @IAlibay @hmacdope @sperezconesa