[gmx-users] Re: REMD analysis
bharat gupta
bharat.85.monu at gmail.com
Fri May 24 08:43:22 CEST 2013
Dear Sir,
I tried a lot to understand the meaning and relation between the .log file
and relica_index file, but I was not able to break the code. I tried to
look into gmx forum for some clue, but didn't find any. So, if possible can
you explain it ...
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
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 of replica_index.xvg
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
On Thu, May 23, 2013 at 11:20 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:
> Looked fine
>
>
> On Thu, May 23, 2013 at 4:13 PM, bharat gupta <bharat.85.monu at gmail.com
> >wrote:
>
> > Sir,
> >
> > What about the description of replica_temp file that I posted in last
> mail.
> > I think that's correct ... If you can comment on that, I can move on with
> > replica_index file...
> >
> >
> > On Thu, May 23, 2013 at 10:58 PM, Mark Abraham <mark.j.abraham at gmail.com
> > >wrote:
> >
> > > 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
> > > >
> > > >
> > > >
> > > >
> > > > --
> > > > 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.
> > > > --
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