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>Regards,<br>sree.<br>
<br><div class="gmail_quote">On Wed, Jul 27, 2011 at 4:58 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">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><div></div><div><br>
<br>
sreelakshmi ramesh wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
dear all ,<br>
I am new to ReMD simulations.And i done a trial run of 100 ps for 7 replicas . if i view the log file for output i get 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 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 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 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 <br>
i had attached only few lines of log file.can any one tel me how to understand the output.<br>
<br>
</blockquote>
<br></div></div>
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>
<br>
Listed are the exchange probabilities between neighboring replicas. Your results indicate that your systems are not exchanging (e.g. probability is zero).<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
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>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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