I should have looked at the format when it writes the time but thanks for your help.
-Swarnendu On Tue, Aug 2, 2011 at 7:07 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > 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 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 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 script > should read the actual time from the previous step in the .log file. > > -Swarnendu > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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