[gmx-users] Re: REMD analysis

[bharat gupta]

Dear Sir,

I checked the md.log and replica_temp.xvg file , what I understood is that
the 'x' means swapping and replica are written that 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







On Thu, May 23, 2013 at 5:21 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> Each md.log has all the information about all replica exchanges, as you can
> see. I suggested you look at your .log and .xvg files a week ago ;-)
> There's no problem if a script post-processes all the identical information
> from each .log file.
>
> Mark
>
>
> On Thu, May 23, 2013 at 9:01 AM, bharat gupta <bharat.85.monu at gmail.com
> >wrote:
>
> > I checked the first 5 md.log files, and the data is exactly the same in
> all
> > of them .... Does it mean there could be problem with demux.pl
> >
> >
> > On Thu, May 23, 2013 at 3:53 PM, Mark Abraham <mark.j.abraham at gmail.com
> > >wrote:
> >
> > > Look at those files. Use diff. They're all the same. Your plots are
> > > probably all showing the first column of each. You want to look at each
> > > column. (And even then the best it can show is that your simulation is
> > not
> > > clearly inadequate.)
> > >
> > > Mark
> > >
> > >
> > > On Thu, May 23, 2013 at 8:48 AM, bharat gupta <
> bharat.85.monu at gmail.com
> > > >wrote:
> > >
> > > > Dear Sir,
> > > >
> > > > Thank you for your reply. But I used the command demux.pl md$.log ,
> > > where
> > > > $= No. of replica. I get the same plot every time. Sorry to ask this
> ,
> > > but
> > > > where am I going wrong ??
> > > > --
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