[gmx-users] Re: REMD analysis

[Mark Abraham]

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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