Sire
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michellab
Sire Molecular Simulations Framework
Hi I created a branch vsites2 and uploaded the changes contained in one commit here: https://github.com/bieniekmateusz/Sire/tree/vsites2 There are some useful code snippets I left in the code that I'll have...
Hello, I'm running ABFE calculations using a version of Sire modified to use Boresch protein-ligand restraints (https://github.com/fjclark/Sire/tree/feature_boresch_restraints). Previously, I have had no issues with the LJ correction, but now I...
Hello, When calculating the free energy change for a perturbation involving only dummy atoms to dummy atoms, MBAR gives exactly zero kcal/ mol, as expected, whereas TI gives positive free...
Hello, I have been testing the `LangevinMiddleIntegrator` functionality in Sire by trying to run 4 fs simulations with HMR but I have been running into numerical instabilities both on CPU...
In the code below molecule numbers start from 2. OpenMMMD.py makes the assumption in centerSolute() that the solute is molnum 1. I get this with devel (commit 3371660dadf6fdc7c1095d69266529c7f4e12845). ``` import...
It would be good to dynamically update the website and documentation using an approach similar to that of BioSimSpace, i.e. sphinx and GitHub pages. This will require splitting @chryswoods personal...
Hi, The N8CIR will shortly be purchasing several Power9 GPU nodes: https://n8cir.org.uk/supporting-research/facilities/nice/ We have access to a node in Newcastle at the moment, and I've managed to install OpenMM following...
# Expected Behavior When converting an AMBER system with non-default scale factors to GROMACS these are reset back to the amber defaults when I think they should be kept. The...
Hello, I am trying to modify the code in Sire to automatically read and recognise virtual sites. So far I am doing this manually, by inserting the parameters of the...
When adding support for triclinic simulation boxes with SOMD I needed to modify [DCDFile.py](https://github.com/michellab/Sire/blob/devel/wrapper/Tools/DCDFile.py). In the file I noticed that periodic boxes are written to file with: ```python boxSize =...