demultiplex script was used to gave one log file of one replica as the input like perl <a href="http://demux.pl">demux.pl</a> md0.log it gave two output files.<br><br><code>replica_index.xvg</code> and replica_temp.xvg.<br>
<br><br>the file replica_temp looks like this <br>0 0 1 2 3 4 5 6 7<br>2 0 1 2 3 4 5 7 6<br>4 0 1 2 3 4 5 7 6<br>6 0 1 2 3 5 4 6 7<br>
8 0 1 2 3 5 4 6 7<br>10 0 1 2 3 5 4 6 7<br>12 0 1 2 4 5 3 6 7<br>14 0 1 2 4 5 3 6 7<br>16 0 1 2 3 5 4 6 7<br>
18 0 1 2 3 5 4 7 6<br>20 0 1 2 3 5 4 7 6<br>22 0 1 2 3 5 4 7 6<br>24 0 1 2 3 5 4 7 6<br>26 0 1 2 3 5 4 6 7<br>
28 0 1 2 3 5 4 6 7<br>30 0 1 2 3 5 4 6 7<br>32 0 1 2 3 5 4 6 7<br>34 0 1 2 3 5 4 6 7<br><br><br>the other index file was passed over trjcat and i concatenated all the other trajectories like this<br>
<br>trjcat -f *.trr -demux replica_index.xvg -o final.trr<br><br>now how to produce temp evolution over time with these concatenated trajectories<br><br>thanks in advance,<br>sree.<br><br><div class="gmail_quote">On Thu, Jul 28, 2011 at 6:53 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"><br>
<br>
sreelakshmi ramesh wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
after having enough exchanges how to follow the temp trajectory of each replica in REMD ? I tried to make it out from edr file of each replica.looks like replica at a particular temp remains almost at a same temp throughout the simulation and does not visit all the other tempratures.any help please.<br>
<br>
<br>
</blockquote>
<br></div>
Trajectories and energy files are ensemble-continuous. Use the <a href="http://demux.pl" target="_blank">demux.pl</a> script to demultiplex the trajectories and produce temperature evolution over time.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Regards,<br>
sree.<div><div></div><div class="h5"><br>
<br>
On Wed, Jul 27, 2011 at 4:58 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
sreelakshmi ramesh wrote:<br>
<br>
dear all ,<br>
I am new to ReMD simulations.And i done a trial run of 100 ps<br>
for 7 replicas . if i view the log file for output i get<br>
something like this for every replica<br>
for one of the replica the log file looks like this<br>
<br>
Replica exchange at step 1000 time 2<br>
Repl 0 <-> 1 dE = 6.793e+02 dpV = 0.000e+00 d = 6.793e+02<br>
Repl ex 0 1 2 3 4 5 6<br>
Repl pr .00 .00 .00 Replica exchange at step<br>
2000 time 4<br>
Repl ex 0 1 2 3 4 5 6<br>
Repl pr .00 .00 .00<br>
Replica exchange at step 3000 time 6<br>
Repl 0 <-> 1 dE = 6.790e+02 dpV = 0.000e+00 d = 6.790e+02<br>
Repl ex 0 1 2 3 4 5 6<br>
Repl pr .00 .00 .00 Replica exchange at step<br>
4000 time 8<br>
Repl ex 0 1 2 3 4 5 6<br>
Repl pr .00 .00 .00<br>
Replica exchange at step 5000 time 10<br>
Repl 0 <-> 1 dE = 6.874e+02 dpV = 0.000e+00 d = 6.874e+02<br>
Repl ex 0 1 2 3 4 5 6<br>
Repl pr .00 .00 .00 Replica exchange at step<br>
6000 time 12<br>
Repl ex 0 1 2 3 4 5 6<br>
Repl pr .00 .00 .00<br>
Replica exchange at step 7000 time 14<br>
Repl 0 <-> 1 dE = 6.535e+02 dpV = 0.000e+00 d = 6.535e+02<br>
Repl ex 0 1 2 3 4 5 6<br>
Repl pr .00 .00 .00 i had attached only few lines of log file.can any one tel me<br>
how to understand the output.<br>
<br>
<br>
I assume you've seen the following?<br>
<br>
<a href="http://www.gromacs.org/__Documentation/How-tos/REMD#__Understanding_REMD-related___Output" target="_blank">http://www.gromacs.org/__<u></u>Documentation/How-tos/REMD#__<u></u>Understanding_REMD-related___<u></u>Output</a><br>
<<a href="http://www.gromacs.org/Documentation/How-tos/REMD#Understanding_REMD-related_Output" target="_blank">http://www.gromacs.org/<u></u>Documentation/How-tos/REMD#<u></u>Understanding_REMD-related_<u></u>Output</a>><br>
<br>
Listed are the exchange probabilities between neighboring replicas.<br>
Your results indicate that your systems are not exchanging (e.g.<br>
probability is zero).<br>
<br>
-Justin<br>
<br>
-- ==============================<u></u>__==========<br>
<br>
Justin A. Lemkul<br>
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ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
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<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
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Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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