The switching protocol has been modified by adding options to save switching conformations (endstate conformations or full switching trajectories). Additionally, the option for performing a 'reverse' unidirectional FEP or NEQ protocol has been added. This PR also provides a script for performing FEP or NEQ for a HiPen system in vacuum.
Todos
[x] modify neq.py and protocol.py: add option to save switching trajectory or endstate conformations
Description
The switching protocol has been modified by adding options to save switching conformations (endstate conformations or full switching trajectories). Additionally, the option for performing a 'reverse' unidirectional FEP or NEQ protocol has been added. This PR also provides a script for performing FEP or NEQ for a HiPen system in vacuum.
Todos
neq.pyandprotocol.py: add option to save switching trajectory or endstate conformationsperform_correction_hipen.pyscriptStatus