[gmx-users] Calculate observed "Acceptance Ratio" from REMD simulation

[henri mone]

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  ...