[gmx-users] Calculate observed "Acceptance Ratio" from REMD simulation
henri mone
henrimone at gmail.com
Sat Aug 21 15:05:40 CEST 2010
Calculate observed "Acceptance Ratio" from REMD simulation
Dear Gromacs users,
I used the Gromacs how-to [1] to setup a REMD simulation. The targeted
acceptance ratio was P_acp=15%, I used the temperature generator
web-service [2] to get the temperature spacing. From the test
simulation I want to calculate the observed acceptance ratio P_obs.
The last md.log file gives a "Replica exchange statistic". I got
following questions regarding on how to calculate P_obs.
1. To get P_obs from simulation I have to calculate the ratio between
the successful exchange and total exchange attempts.
Is this correct? I checked several papers and books (Frenkel/Smit,
etc.), I only found the formula how to calculate the temperature
spacing given P_acp. But I couldn't find a formula or definition how
to calculate P_obs from a simulation. Is the above definition of P_obs
correct?
2. The md.log file "Replica exchange statistic" gives in my case
following summary [3]. For temperature T0 to T1 there wehre 664
successful exchanges. The number of exchange attempts were 1213. The
ratio 664/1213 gives 55%. Would the P_obs=55% , is this correct?
3. A observed ratio of P_obs=50% given a targeted acceptance ratio of
P_acp=15% is quite high.
What can be the reason for this large discrepancy?
4. Could the Gromacs users, admin etc. please add some more
information to the REMD Howto [1]. In particular regarding how to
calculate P_obs?
It would be a really useful for the Gromacs users.
Can I as a Gromacs user add some more information to the howto or do I
need a login?
I would appreciate any help.
Thanks,
Henri
1: Replica-Exchange Molecular Dynamics howto
http://www.gromacs.org/Documentation/How-tos/REMD
2: Temperature generator for REMD-simulations
http://folding.bmc.uu.se/remd/
3: "md.log" file summary
Replica exchange statistics
Repl 2425 attempts, 1213 odd, 1212 even
Repl average probabilities:
Repl 0 1 2 3 4 5 6 7 8 9 10 ...
Repl .55 .55 .55 .56 .56 .54 .56 .56 .56 .56 ...
Repl number of exchanges:
Repl 0 1 2 3 4 5 6 7 8 9 10 ...
Repl 664 684 667 692 659 627 699 688 699 683 ...
Repl average number of exchanges:
Repl 0 1 2 3 4 5 6 7 8 9 10 ...
Repl .55 .56 .55 .57 .54 .52 .58 .57 .58 .56 ...
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