[gmx-users] HREMD output

[Mark Abraham]

Hi,


On Wed, Jan 20, 2016 at 3:07 PM Shyno Mathew <sm3334 at columbia.edu> wrote:

> Dear all,
>
> Using demux.pl script, I created the co-ordinate trajectories.


Unlike some other MD packages, GROMACS REMD trajectories are written such
that they are continuous with respect to ensemble index. So only demux if
you want continuous with respect to replica index.

When I plot
> the rmsd for the lowest replica, I see huge jumps (0.4 nm to 0.6nm) at few
> steps.


If you've demuxed, your trajectory should be free of jumps, so this sounds
like a normal issue of dealing with periodicity (
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
)


> 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?
>

Probably so. I forget what the script does for the two .xvg files it
writes, but you can work it out by inspecting your .log files to see what
exchanges actually occured over the first few exchange intervals.

Mark


>
> 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
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