Rohit Farmer wrote:
Hi there,
I just run a REMD using just two replicas and extracted the results
using the following
grep Repl md0.log
Initializing Replica Exchange
Repl There are 2 replicas:
Repl Using Constant Pressure REMD.
Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal
ensemble
Repl 0 1
Repl T 300.0 310.7
Repl p 1.00 1.00
Repl
Repl exchange interval: 1000
Repl random seed: 13622
Repl below: x=exchange, pr=probability
Replica exchange at step 1000 time 2
Repl 0 <-> 1 dE = 2.813e+01 dpV = 0.000e+00 d = 2.813e+01
Repl ex 0 1
Repl pr .00
Replica exchange at step 2000 time 4
Repl ex 0 1
Repl pr
Replica exchange at step 3000 time 6
Repl 0 <-> 1 dE = 3.251e+01 dpV = 0.000e+00 d = 3.251e+01
Repl ex 0 1
Repl pr .00
Replica exchange at step 4000 time 8
Repl ex 0 1
Repl pr
Replica exchange at step 5000 time 10
Repl 0 <-> 1 dE = 2.442e+01 dpV = 0.000e+00 d = 2.442e+01
Repl ex 0 1
Repl pr .00
Replica exchange at step 6000 time 12
Repl ex 0 1
Repl pr
Replica exchange at step 7000 time 14
Repl 0 <-> 1 dE = 1.712e+01 dpV = 0.000e+00 d = 1.712e+01
Repl ex 0 1
Repl pr .00
..................
..................
.................
Replica exchange statistics
Repl 49 attempts, 25 odd, 24 even
Repl average probabilities:
Repl 0 1
Repl .00
Repl number of exchanges:
Repl 0 1
Repl 0
Repl average number of exchanges:
Repl 0 1
Repl .00
I couldn't understand the result according to this output it seems no
exchange has taken place. What should be the output if an exchange has
occurred.
The exchange probability would be nonzero. You have a rather large value of dE
between the two replicates; exchange is unlikely.
-Justin
--
========================================
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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