Currently, the equilibration step is run serial, each λ window at time. This is slow and may lead to crashes (eg, #84 and #97). To fix that, equilibration should be run using gmx mdrun -multidir.
I am writing that code in a "dirty" way for now, which means use the current runall.sh logic, changing only the relevant code.
Later, I hope to rewrite the run script from the ground up, including the parallel equilibration.
Currently, the equilibration step is run serial, each λ window at time. This is slow and may lead to crashes (eg, #84 and #97). To fix that, equilibration should be run using
gmx mdrun -multidir.I am writing that code in a "dirty" way for now, which means use the current
runall.shlogic, changing only the relevant code.Later, I hope to rewrite the run script from the ground up, including the parallel equilibration.