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General question--how should topology proposals be organized, and how should they be matched with `System` construction?
Currently, under the small molecule scheme, there is:
- `Transformation`
- `…
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I was actually hoping to have an example that packaged the entire FreeSolv small molecule database into a single OpenMM ForceField-compatible ffxml file, since we could use this for various OpenMM-dep…
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Hi,
I have implemented a custom non bonded force into openMM and am now trying to optimize it with ForceBalance. However when run with my custom forcefeild and targets I get the error:
File "/usr/lib6…
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It may not make sense to implement all of these. Will update as I try each of them. Please add any other potentially useful programs to this list (I've ignored programs like pdb2gmx and antechamber si…
ctk3b updated
9 years ago
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It might be nice so that users can immediately benchmark their systems.
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I was thinking we ought to take five minutes to think about possible issues that we might encounter when eventually working with small molecule trajectories.
Obviously we would need things like an …
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I'm starting to work on a tool for fixing problems in PDB files. The goal is to have something that can load a file downloaded straight from RCSB, fix any problems with it in a completely automated w…