[gmx-users] Re: REMD analysis

[Mark Abraham]

It's a demux. One might want trajectories to be at constant temperature, or
constant replica. The two files define the (mutually inverse) mappings
between those representations. So one file tells you which replica is at
each temperature, and the other which temperature holds each replica.
Nobody's ever written down anything about which is which, so like I said a
week back, look at the first few exchanges, see how those are represented
in the files, and decide for yourself which file's columns/rows have useful
information you want to look at. And do write that decision down! :-)

Mark


On Thu, May 23, 2013 at 2:55 PM, simula_460 <bharat.85.monu at gmail.com>wrote:

> 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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> http://gromacs.5086.x6.nabble.com/REMD-analysis-tp5008199p5008481.html
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