I should have looked at the format when it writes the time but thanks for your help.<br><br>-Swarnendu<br><br><div class="gmail_quote">On Tue, Aug 2, 2011 at 7:07 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div text="#000000" bgcolor="#FFFFFF"><div class="im">
On 3/08/2011 8:19 AM, Swarnendu Tripathi wrote:
<blockquote type="cite">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" target="_blank">demux.pl</a> script it does not read the
actual time from the .log file. This is for gromacs-4.0.7.<br>
</blockquote>
<br></div>
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.<br>
<br>
Thanks for the report.<br><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
<br>
<blockquote type="cite">
<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" target="_blank">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" target="_blank">demux.pl</a>
script should read the actual time from the previous step in the
.log file.<br>
<br>
-Swarnendu<br>
<br>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div></div></div>
<br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br>