I checked the md.log and replica_temp.xvg file , what I understood is that the 'x' means swapping and replica are written this way. For eg. Replica exchange at step 1000 time 2 Repl 0 <-> 1 dE = -1.067e+00 Repl ex 0 x 1 2 3 4 5 6 7 8 9 10 11 12 x 13 Repl pr 1.0 .01 .68 .21 .05 .09 .26
output in replica_temp file will be 1 0 2 3 4 5 6 7 8 9 10 11 13 12 It means that replica 1 at higher temp. exchange with the one in lower temp 0. Replica exchange at step 2000 time 4 Repl ex 0 1 x 2 3 4 5 6 7 8 9 10 11 12 13 Repl pr .91 .32 .00 .07 .18 .08 output in replica_temp file will be 1 0 2 3 4 5 6 7 8 9 10 11 13 12 2 0 1 3 4 5 6 7 8 9 10 11 13 12 [order is from low to high temp] But I am not able to understand for replica_index file :- for the above two time steps here's the output :- 0 0 1 2 3 4 5 6 7 8 9 10 11 12 13 2 1 0 2 3 4 5 6 7 8 9 10 11 13 12 4 1 2 0 3 4 5 6 7 8 9 10 11 13 12 The time step four is different here, I don't know why ?? Ideally the output should be same in both files, I suppose ?? Also, I tried to plot for each column separately , here I want to clarify that whether each column represents the time evolution of each replica over time. For eg. the second column should represent the temp evolution for replica No. 0 wrt to time. Presuming that I understood it correctly, I plotted the temp. evolution over time of all replicas separately . Here's the replica_temp plot for replicas 0 to 13. https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png -- View this message in context: http://gromacs.5086.x6.nabble.com/REMD-analysis-tp5008199p5008481.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
