This package is a python library with tools for the Molecular Simulation - Software Gromos. It allows you to easily set up, manage and analyze simulations in python.
In the GROMOS repdat format, one row corresponds to one exchange between replicas i and j. In practice, the potentials of the end-states are written "before" the exchange, and correspond to the coordinates of the s_value i before they are exchanged. However, the coord_ID is written "after" the exchange has taken place, meaning that in a single row the potentials don't correspond to the coord_ID.
One of the goals of the ExpandedRepdat is to be able to track the potentials of a coordinates trajectory, and therefore the fix to make them match is included here. This should give the same energy values (plus the eoffs) as using get_replica_traces on a Repdat
In the GROMOS repdat format, one row corresponds to one exchange between replicas i and j. In practice, the potentials of the end-states are written "before" the exchange, and correspond to the coordinates of the s_value i before they are exchanged. However, the coord_ID is written "after" the exchange has taken place, meaning that in a single row the potentials don't correspond to the coord_ID.
One of the goals of the
ExpandedRepdatis to be able to track the potentials of a coordinates trajectory, and therefore the fix to make them match is included here. This should give the same energy values (plus the eoffs) as usingget_replica_traceson aRepdat