[gmx-users] REMD, demux after 100 ns per replica

[Mark Abraham]

Hi,

Yes, I have seen this. Unfortunately that script dates from the days when
10ns was a long run, and like most things in GROMACS, hasn't seen much love
since one of the developers was actively using it. If you can test your
fixed version and want to contribute it back, you can follow the
instructions at http://www.gromacs.org/Developer_Zone/Git/Gerrit

Mark
On Apr 16, 2014 5:52 PM, "aperez" <a.pervilla at gmail.com> wrote:

> Hi all,
>
> Today I have experienced a problem with the demux script applied in a
> replica exchange simulation.
> I have 16 replicas, and for each replica I have about 120 ns of MD.
> When I executed the script demux.pl on the log file, I noticed that the
> first column of the replica_*.xvg files had a problem after 100000 ps (100
> ns).
> I essentially got this:
>
> ...
> 99999.6       15   11   13    8    0   14    6    7    5   10    4    1
>  9
> 2    3   12
> 99999.8       11   15    8   13    0   14    6    7    5   10    1    4
>  9
> 2   12    3
> 100000        11   15    8   13    0   14    6    7    5   10    1    9
>  4
> 2   12    3
> 100000        11   15   13    8   14    0    6    7   10    5    1    9
>  4
> 2    3   12
> 100000        11   15   13    8   14    0    6   10    7    5    1    9
>  4
> 2    3   12
> 100000        15   11   13    8   14    0    6   10    7    5    1    9
>  4
> 2    3   12
> 100000        15   13   11    8   14    0    6   10    7    5    1    9
>  4
> 3    2   12
> 100001        13   15   11    8   14    0    6   10    7    5    9    1
>  4
> 3    2   12
> 100001        13   15   11    8   14    0    6    7   10    9    5    4
>  1
> 2    3   12
> ...
>
> As you can see, after 100 ns the time step precision changes, loosing the
> decimal place.
> Does it mean that my 'demuxed' trajectories after 100 ns will experience
> unexpected jumps? Because I saw this in my RMSD calculations...
>
> This problem was fixed editing the demux.pl, in which this script reads
> instead of the time ($log_line[6]), the frame multiplied by the dt -in my
> case 2 fs- ((0.002)*$log_line[4]) from the log file, and also changing the
> printf like this:
>
> printf(NDX "%-20g",$t) ==> print (NDX "%-10.2f",$t)
> printf(TEMP "%-20g",$t) ==> printf(TEMP "%-10.2f",$t)
>
> However I am curious to know if you had already encountered such problem.
> Thanks a lot for any possible comment,
> Andrea
>
>
>
>
>
> -----
> Andrea Pérez-Villa
> PhD student in Physics and Chemistry of Biological Systems
> SISSA, Italy
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/REMD-demux-after-100-ns-per-replica-tp5015885.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
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