[gmx-users] bug in demux.pl
Swarnendu Tripathi
stripat1 at kent.edu
Wed Aug 3 00:19:46 CEST 2011
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.
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
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