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.abra...@gmail.com>wrote: > Looked fine > > > On Thu, May 23, 2013 at 4:13 PM, bharat gupta <bharat.85.m...@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.abra...@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.m...@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. > > > > -- > > > > gmx-users mailing list gmx-users@gromacs.org > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > > * Please don't post (un)subscribe requests to the list. Use the > > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > -- > > > gmx-users mailing list gmx-users@gromacs.org > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > * Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
