Support for the string method with swarms of trajectories in GROMACS
As discussed with the GROMACS developers, we should make sure that we can easily implement enhanced sampling/ensemble methods on top of GROMACS. This feature request specifically outlines what is needed to run the string method with swarms of trajectories. The method will work as a showcase of path sampling and ensemble methods with GROMACS in general.
This feature request is based on the following design document: https://docs.google.com/document/d/10qGoDYoyHSlXPP263egWr8edUe8kvUQURgUdfIqHjfM/edit?usp=sharing, also attached below.In practice we need to do the following:
- Make sure the colvars package works with GROMACS for this purpose. We need to be able to restrain a system to some collective variable. Optionally we can use pull code for this.
- Assert that the python api can start and load trajectories as intended and wait for the simulations to finish.
- Reset the random seed in simulations starting from the same tpr file (currently only supported with the '-multi' option).
- Don't output the first frame for many replicas starting from the same initial coordinates. In practice this would reduce the total size of xtc files by 50 %.