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OpenBioSim
Sire Molecular Simulations Framework
This PR closes #194 by skipping BioSimSpace position restraint include directives when parsing GROMACS topology files. I'm not sure if there is a more general way of fixing this issue,...
I'm not 100% sure if this is the cause, but I'm seeing repeated failures in the environment setup stage for my `sire-emle` build on macOS. In the log I see:...
The presence of include directives such as the following cause the parser to fail with no informative error. ``` #include "posre_0001.itp" ``` These files are written by BioSimSpace for when...
**Describe the bug** This might more of a feature request rather than a bug report _per se_, since I don't think `mol.move().align()` was orignally designed to work with proteins. I...
A suggestion prompted by a reviewer - add a function that sorts loaded trajectory frames in different ways, e.g. could sort based on the timestamp of the trajectory files, the...
While we can write Gromacs FEP topology files for merged molecules, we cannot read back those files. We should add support for reading Gromacs topology files that contain merged molecules.
We currently set `cmake_minimum_required` to `3.3.0`. CMake support for
**Describe the bug** I've recently been trying to implement multiple distance restraints for absolute binding free energy calculations in BioSimSpace and SOMD ([modified BSS](https://github.com/fjclark/biosimspace-openbiosim/tree/feature_mdr), [modified sire](https://github.com/fjclark/sire-openbiosim/tree/feature_permanent_mdr), and an [example of...
I hadn't realised that the PME implementation existed in a completely separate class, so the torsion fix is missing there. * I confirm that I have merged the latest version...
Based of Boresch restraints for RF in src/libs/SireMove/openmmfrenergyst.cpp and https://github.com/OpenBioSim/sire/commit/43ed4bc57fa9f407e13621de1420550c154131c9 * I confirm that I have merged the latest version of `devel` into this branch before issuing this pull request...
