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

[aperez]

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
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