[gmx-users] Re: REMD analysis

[simula_460]

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




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