[gmx-users] HREMD output

[Shyno Mathew]

Dear all,

Using demux.pl script, I created the co-ordinate trajectories. When I plot
the rmsd for the lowest replica, I see huge jumps (0.4 nm to 0.6nm) at few
steps. To explain this behavior I need to find out the temperature at each
step.

Now to see the temperature for each step, I need to look for 0 in each row
in replica_temp.xvg and see which column 0 belongs to. Is this correct?

Following are the first three lines of the replica_temp.xvg file. I have 32
replicas, and there is no exchange in the first 5ns. If I look at step3
(frame 5002), replica 0 is in column 4, meaning replica 0 has the
temperature of replica 2?

0                       0    1    2    3    4    5    6    7    8    9
10   11   12   13   14   15   16   17   18   19   20   21   22   23   24
25   26   27   28   29   30   31
5000                    0    2    1    4    3    5    6    8    7    9
10   11   12   13   14   15   16   18   17   19   20   22   21   24   23
26   25   27   28   30   29   31
5002                    1    2    0    4    3    5    6    8    7    9
10   11   12   13   14   15   16   18   17   19   21   22   20   25   23
27   24   26   28   30   29   31


thanks,
Shyno

-- 
Shyno Mathew
PhD Candidate
Department of Chemical Engineering
Graduate Assistant
Office of Graduate Student Affairs
The Fu Foundation School Of Engineering and Applied Science
Columbia University