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Hi Espaloma Devs,
I am exploring the use of Espaloma (with RdKit under the hood) to describe a protein + ligand complex.
When comparing system XML files from an (unsolvated) Espaloma described …
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Hi,
I'm working on implementing buffered force mixing (https://pubs.acs.org/doi/10.1021/jp405974b) in openMM, where the use case would be having an ML potential compute forces on a subset of the sy…
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In order to have assurance that Open Force Field represents Amber parameters in the correct manner, energy evaluations of Amber-minimized structures will be carried out in Amber and OpenMM simulation …
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## FEATURE REQUEST
### Inspiration
Recording the labeled positions for Deuterium labled compounds can be ambiguous. Update the documentation to clarify that TraceBase uses the convention where…
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There are cases where because of slashing, nomination pool members have contribution less than ED. When this happens, we should have a way to reap these accounts. This could be exposed via a permissio…
Ank4n updated
3 weeks ago
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This isn't a bug, but I wanted to ask about the definition of "annihilation" as implemented in [`sire.morph.annihilate()`](https://sire.openbiosim.org/api/morph.html#sire.morph.annihilate).
The doc…
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In alchemical free energy calculations, we often need to define torsions and angles in a way that may introduce numerical instabilities (eg. morphing into nitriles, ring opening/closing, etc.). Typica…
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So, I have the following problem. I want to restrain individual particles to be within X nanometers from the center of mass of a different molecule.
I have tried to come up with a solution with the…
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Dear moltemplate developers,
I am trying to simulate Anthracene with OPLS-AA force field in LAMMPS.
To generate the data files needed I assigned the following atom types:
- 90 (Aromatic C) fo…