On 2010-08-21 15.05, henri mone wrote:
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?
Good question. We used two force fields (OPLS and GROMOS) for the
development. We did however use Berendsen thermostats, which is not a
good idea, and this might induce a deviation, but I would expect it to
be small. The most obvious thing could be that the system used is not
the one for which you input parameters on the webserver. The webserver
wants the number of water molecules, if you supplied the number of
atoms, that would give you a factor of three in energy.
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 ...
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
[email protected] http://folding.bmc.uu.se
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