Hi,<br><br>I am not sure if this problem has been solved or discussed before.<br><br>I found that when I use the <a href="http://demux.pl">demux.pl</a> script it does not read the actual time from the .log file. This is for gromacs-4.0.7.<br>
<br>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 <a href="http://demux.pl">demux.pl</a> script reads the time from the "Replica exchange" phrase as "<span style="background-color: rgb(255, 255, 255);">1.19999e+06</span>". Same thing repeats in the following steps which is not right.<br>
==================================================================<br> Step Time Lambda<br> 299998000 <span style="background-color: rgb(255, 255, 102);">1199992.12500</span> 0.00000<br>
<br> Energies (kJ/mol)<br> G96Bond G96Angle Proper Dih. Improper Dih. LJ-14<br> 1.58180e+03 1.49412e+03 7.67393e+02 3.69239e+02 -2.78302e+02<br> Coulomb-14 LJ (SR) Coulomb (SR) Potential Kinetic En.<br>
-2.39467e+00 8.01055e+01 -1.05400e+01 4.00143e+03 4.06353e+03<br> Total Energy Temperature Pressure (bar)<br> 8.06496e+03 4.51898e+02 0.00000e+00<br><br>Replica exchange at step 299998000 time <span style="background-color: rgb(153, 255, 153);">1.19999e+06</span><br>
Repl 7 <-> 8 dE = 1.607e-01<br>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<br>Repl pr .79 1.0 1.0 .85 1.0 .98 .98 .90 1.0 1.0 .90 <br>
<br> Step Time Lambda<br> 299999000 1199996.12500 0.00000<br><br> Energies (kJ/mol)<br> G96Bond G96Angle Proper Dih. Improper Dih. LJ-14<br> 1.42588e+03 1.43257e+03 7.64199e+02 3.39804e+02 -7.50646e+02<br>
Coulomb-14 LJ (SR) Coulomb (SR) Potential Kinetic En.<br> -2.96172e+00 9.62908e+01 -1.95152e+01 3.28563e+03 4.16581e+03<br> Total Energy Temperature Pressure (bar)<br> 7.45144e+03 4.63272e+02 0.00000e+00<br>
<br>Replica exchange at step 299999000 time 1.2e+06<br>Repl 8 <-> 9 dE = 2.023e-01<br>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<br>
Repl pr 1.0 .98 .66 1.0 .82 1.0 .92 .93 .79 1.0 .96 1.0<br><br>========================================================================================<br>
<br>As a result my "replica_index.xvg" looks like this which is not right.<br>========================================================================================<br>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<br>
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<br>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<br>
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<br>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<br>
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<br>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<br>
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<br>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<br>
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<br>=========================================================================================<br>
<br>Due to the problem in precision, time step repeats. The <a href="http://demux.pl">demux.pl</a> script should read the actual time from the previous step in the .log file.<br><br>-Swarnendu<br>