Dear researchers,

When performing REMD/REST on Gromacs, we use this "demux md0.log" command to produce two files: replica_temp.xvg and replica_index.xvg. "replica_temp.xvg" allows us to see the diffusion of each replica in temperature space while "replica_index.xvg" allows us to reconstruct continuous trajectory for each replica via "gmx_mpi trjcat -f topol*.xtc -demux replcia_index.xvg" and we should have demux trajectories named 0_trajout.xtc, ..., x_trajout.xtc for each replica (Please correct me if I'm wrong).

My understanding is that for each x_trajout.xtc it is the continuous trajectory for the replica started at the "order x". However, when I checked the demux trajectories, only the very first one (0_trajout) seems to reflect this. Here is how I check the demux trajectories: first I plot the diffusion of (let's say) replica 10 in the temperature space, and then I find the specific times when replica 10 is at temperature 10 (the eleventh temperature). After this, I made plots of order parameter (RMSD, native contact or anything else) versus time for topol0.xtc and for 0_trajout.xtc. At the specific times I found earlier, the order parameter for trajectory at temperature 10 and the trajectory for replica 10 should be the same. However, except for the very first replica, other demux replicas do not reflect this. Does anyone have an idea? Thanks in advance!

Regards,

Peiyin