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.abra...@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.m...@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.abra...@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.m...@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 ?? > > > > -- > > > > 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