sreelakshmi ramesh wrote:
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.
Trajectories and energy files are ensemble-continuous. Use the demux.pl script
to demultiplex the trajectories and produce temperature evolution over time.
-Justin
Regards,
sree.
On Wed, Jul 27, 2011 at 4:58 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
sreelakshmi ramesh wrote:
dear all ,
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
for one of the replica the log file looks like this
Replica exchange at step 1000 time 2
Repl 0 <-> 1 dE = 6.793e+02 dpV = 0.000e+00 d = 6.793e+02
Repl ex 0 1 2 3 4 5 6
Repl pr .00 .00 .00 Replica exchange at step
2000 time 4
Repl ex 0 1 2 3 4 5 6
Repl pr .00 .00 .00
Replica exchange at step 3000 time 6
Repl 0 <-> 1 dE = 6.790e+02 dpV = 0.000e+00 d = 6.790e+02
Repl ex 0 1 2 3 4 5 6
Repl pr .00 .00 .00 Replica exchange at step
4000 time 8
Repl ex 0 1 2 3 4 5 6
Repl pr .00 .00 .00
Replica exchange at step 5000 time 10
Repl 0 <-> 1 dE = 6.874e+02 dpV = 0.000e+00 d = 6.874e+02
Repl ex 0 1 2 3 4 5 6
Repl pr .00 .00 .00 Replica exchange at step
6000 time 12
Repl ex 0 1 2 3 4 5 6
Repl pr .00 .00 .00
Replica exchange at step 7000 time 14
Repl 0 <-> 1 dE = 6.535e+02 dpV = 0.000e+00 d = 6.535e+02
Repl ex 0 1 2 3 4 5 6
Repl pr .00 .00 .00
i had attached only few lines of log file.can any one tel me
how to understand the output.
I assume you've seen the following?
http://www.gromacs.org/__Documentation/How-tos/REMD#__Understanding_REMD-related___Output
<http://www.gromacs.org/Documentation/How-tos/REMD#Understanding_REMD-related_Output>
Listed are the exchange probabilities between neighboring replicas.
Your results indicate that your systems are not exchanging (e.g.
probability is zero).
-Justin
--
==============================__==========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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