BioSimSpace
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michellab
Code and resources for the EPSRC BioSimSpace project.
As far as I am aware Sire doesn't currently have data structures to describe virtual sites. Virtual sites are becoming more and more popular and are found in a growing...
This PR fixes the offset used when injecting the inclusion of external `posre*.itp` files into a GROMACS topology. The logic used previously meant that the offset was incorrect, meaning that...
Opening this thread for a discussion about strategies for migrating Sire and BioSimSpace to the [OpenBioSim](https://github.com/OpenBioSim) GitHub organisation. ### Timing Do we want to do this ASAP, or coincide with...
**Is your feature request related to a problem? Please describe.** Hi, I tried to use BSS to run MD simulations for a protein-ligand complex using Gromacs. Looking at the configuration...
Hello! I hope you are doing well! We are a security research team. Our tool automatically detected a vulnerability in this repository. We want to disclose it responsibly. GitHub has...
Hi, I'm attempting to use HMR with FEP calculations for longer sampling times. I noticed when using the repartitionHydrogenMass method that the hydrogen masses in the [atomtypes] directive of the...
Hello, I have run into an issue when trying to load an alchemical system generated by a GROMACS run, squashing it and writing it out as an AMBER rst7 (writing...
Is it possible to add ions to an already solvated system, without adding any more water molecules?
**Is your feature request related to a problem? Please describe.** A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] **Describe the solution you'd...
