[gmx-users] Reg: REMD result

[Justin A. Lemkul]

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

========================================