[gmx-users] bug in demux.pl
Mark Abraham
Mark.Abraham at anu.edu.au
Wed Aug 3 01:07:47 CEST 2011
On 3/08/2011 8:19 AM, Swarnendu Tripathi wrote:
> Hi,
>
> I am not sure if this problem has been solved or discussed before.
>
> I found that when I use the demux.pl <http://demux.pl> script it does
> not read the actual time from the .log file. This is for gromacs-4.0.7.
It reads the values fine, it just writes them in a limited-width format.
You can find two occurrences of "%-8g" early in the script. Replace them
with something like "%-20g" and things will work fine.
Thanks for the report.
Mark
>
> These are few lines from one of the .log file for my replica exchnage
> simulation. For example in the second line below the actual time is
> "1199992.0" in ps. However, the demux.pl <http://demux.pl> script
> reads the time from the "Replica exchange" phrase as "1.19999e+06".
> Same thing repeats in the following steps which is not right.
> ==================================================================
> Step Time Lambda
> 299998000 1199992.12500 0.00000
>
> Energies (kJ/mol)
> G96Bond G96Angle Proper Dih. Improper Dih.
> LJ-14
> 1.58180e+03 1.49412e+03 7.67393e+02 3.69239e+02
> -2.78302e+02
> Coulomb-14 LJ (SR) Coulomb (SR) Potential
> Kinetic En.
> -2.39467e+00 8.01055e+01 -1.05400e+01 4.00143e+03
> 4.06353e+03
> Total Energy Temperature Pressure (bar)
> 8.06496e+03 4.51898e+02 0.00000e+00
>
> Replica exchange at step 299998000 time 1.19999e+06
> Repl 7 <-> 8 dE = 1.607e-01
> Repl ex 0 1 x 2 3 x 4 5 x 6 7 x 8 9 x 10 11 x
> 12 13 x 14 15 x 16 17 x 18 19 x 20 21 x 22 23
> Repl pr .79 1.0 1.0 .85 1.0
> .98 .98 .90 1.0 1.0 .90
>
> Step Time Lambda
> 299999000 1199996.12500 0.00000
>
> Energies (kJ/mol)
> G96Bond G96Angle Proper Dih. Improper Dih.
> LJ-14
> 1.42588e+03 1.43257e+03 7.64199e+02 3.39804e+02
> -7.50646e+02
> Coulomb-14 LJ (SR) Coulomb (SR) Potential
> Kinetic En.
> -2.96172e+00 9.62908e+01 -1.95152e+01 3.28563e+03
> 4.16581e+03
> Total Energy Temperature Pressure (bar)
> 7.45144e+03 4.63272e+02 0.00000e+00
>
> Replica exchange at step 299999000 time 1.2e+06
> Repl 8 <-> 9 dE = 2.023e-01
> Repl ex 0 x 1 2 x 3 4 x 5 6 x 7 8 9 10 x 11 12
> x 13 14 x 15 16 x 17 18 x 19 20 x 21 22 x 23
> Repl pr 1.0 .98 .66 1.0 .82 1.0
> .92 .93 .79 1.0 .96 1.0
>
> ========================================================================================
>
> As a result my "replica_index.xvg" looks like this which is not right.
> ========================================================================================
> 1.19996e+06 11 9 22 12 10 21 5 23 17 7 19
> 8 3 1 15 0 13 6 20 14 4 2 16 18
> 1.19996e+06 9 11 12 22 21 10 23 5 7 17 8
> 19 1 3 0 15 6 13 14 20 2 4 18 16
> 1.19997e+06 9 12 11 21 22 23 10 7 5 8 17
> 1 19 0 3 6 15 14 13 2 20 18 4 16
> 1.19997e+06 12 9 21 11 23 22 7 10 8 5 1
> 17 0 19 6 3 14 15 2 13 20 18 16 4
> 1.19998e+06 12 21 9 23 11 22 7 8 10 5 1
> 0 17 6 19 14 3 2 15 13 20 16 18 4
> 1.19998e+06 21 12 23 9 22 11 8 7 10 5 0
> 1 6 17 19 14 2 3 13 15 16 20 4 18
> 1.19998e+06 21 23 12 22 9 8 11 10 7 5 0
> 6 1 19 17 2 14 13 3 16 15 4 20 18
> 1.19999e+06 23 21 22 12 9 8 10 11 5 7 6
> 0 19 1 2 17 13 14 16 3 4 15 18 20
> 1.19999e+06 23 22 21 9 12 10 8 5 11 6 7
> 19 0 2 1 13 17 16 14 4 3 18 15 20
> 1.2e+06 22 23 9 21 10 12 5 8 11 6 19
> 7 2 0 13 1 16 17 4 14 18 3 20 15
> =========================================================================================
>
> Due to the problem in precision, time step repeats. The demux.pl
> <http://demux.pl> script should read the actual time from the previous
> step in the .log file.
>
> -Swarnendu
>
>
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