Hello,
Could anyone please explain the difference between replica_index and replica_temp when you run demux? I tried finding resources but could not find many details about it.
I am using replica_index.xvg to analyse the free energy surface. Could you please let me know if I am making a huge blunder?
Thank you, Regards
Karan V
Hi,
They are mutually inverse:
Replica_temp.xvg shows the diffusion of each replica in temperature space, i.e. each replica (column) is at what temperature. Replica_index.xvg shows the opposite, i.e. each temperature (column) is at which replica. You can use either of them to demux the trajectory (continuous in time or at fixed temperature) based on your need. By default, the trajectories are written for fixed temperature. You can do “trjcat + replica_index.xvg” to export a continuous trajectory in time.
Best,
Hadi.