Sire
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michellab
Sire Molecular Simulations Framework
When adding functionality to SOMD multiple files need to be updated: [openmmmdintegrator.h](https://github.com/michellab/Sire/blob/devel/corelib/src/libs/SireMove/openmmmdintegrator.h), [openmmmdintegrator.cpp](https://github.com/michellab/Sire/blob/devel/corelib/src/libs/SireMove/openmmmdintegrator.cpp), [openmmfrenergyst.h](https://github.com/michellab/Sire/blob/devel/corelib/src/libs/SireMove/openmmfrenergyst.h), [openmmfrenergyst.cpp](https://github.com/michellab/Sire/blob/devel/corelib/src/libs/SireMove/openmmfrenergyst.cpp), [openmmfrenergydt.h](https://github.com/michellab/Sire/blob/devel/corelib/src/libs/SireMove/openmmfrenergydt.h), [openmmfrenergydt.cpp](https://github.com/michellab/Sire/blob/devel/corelib/src/libs/SireMove/openmmfrenergydt.cpp). These files contain a lot of duplicated functionality that would be better served...
The exact Sire version used is no written in the SOMD outputs. This would be useful for debugging purposes.
Hi, I am running an MD simulation of a protein-ligand complex using SOMD. But I a am unable to control the information the simulation outputs, and therefore I cannot perform...
Hello, I have been running somd-freenrg calculations I often obtained the following warning when analyzing my results "#WARNING SUBSAMPLING ENERGIES RESULTED IN LESS THAN 50 SAMPLES, CONSIDER RERUN WITHOUT SUBSAMPLE...
I am trying to create a Virtual Site (VS) in Sire with parameters that are stored in a "virtual-sites" property of a molecule. I am testing my implementation by running...
SOMD can be used to generate an example configuration file with default parameters, i.e. ```bash $HOME/sire.app/bin/somd --help-config ``` However, for parameters that have units, e.g. times, temperatures, etc., the unit...
We should hopefully be able to create a Windows pipeline for Sire, which would allow us to generate a Conda package for Windows.
When loading a molecule form amber prm7 and rst7 and then writing it out to mol2, the atom types are set to dummy, this means the mol2 file cannot be...
I'm not sure if I'm missing something, but is there a reason why "name" is used to identify perturbed atoms in the SOMD pert file. Since this isn't unique it...
Currently SOMD requires an _exact_ AMBER water topology naming convention. This is down to the way that it applies constraints, e.g. from [openmmfrenergyst.cpp](https://github.com/michellab/Sire/blob/devel/corelib/src/libs/SireMove/openmmfrenergyst.cpp): ```cpp if (flag_constraint == NONE) { //JM...