[gmx-users] poor performance in Hemiltonian Replica Exchange

Michael Shirts mrshirts at gmail.com
Thu May 10 20:20:44 CEST 2012

4.6 will include Hamiltonian replia exchange functionality built into
the MPI version.

Currently the description of the error is very vague -- if you can
write up what exactly the numbers are, and what they should be, with
files that exactly replicate the error, then I can take a look.  But
unless I can reproduce the error you are describing out of the box,
its unlikely I will be able to find it.

Additionally, it would be easiest if the files were deposited as a
redmine bug report, so that the information is centrally located.


On Thu, May 10, 2012 at 12:23 PM, francesco oteri
<francesco.oteri at gmail.com> wrote:
> Dear gromacs users,
> I performed a Hemiltonian Replica Exchange (i.e. replica exchange where each
> replica has a init_lambda=0, delta_lambda=0 and init_lambda ranging
> uniformely from 0 to 1).
> Since I have only ten fixed discrete lambda, I run a Temperature Replica
> Exchange where, for each replica I generated a .top file with the parameter
> rescaled through a
> python script ( in practice I did through python the same thing gromacs is
> supposed to do with the H-REM previously described). Now gromacs complained
> because
> every replica has the same setup, so I changed the temperatures using very
> close values (300.0001K,
>  300.0002K,300.0003K,300.0004K,300.0005K,300.0006K,300.0007K,300.0008K, 300.0009K)
> With this setup the simulation runs fine and I expect to have similar
> result.
> Then I compared the results observing two phenomena:
> 1) In the second case exchange rate is 100%, while in the first case I have
> an exchange rate close to 30%.
> Does it rise  because the temperatures are too close?
> 2) The second setup is 3x faster!
> In particular I observe an imbalance between PME and force calculation
> ranging from 10% to 60%.
> I tried to run each replia indipendently (a different mdrun instance for
> each .tpr file) but still I observe the same performance slowdown.
> I guess the free energy impairs the efficient force calculation, but I dont
> understand why.
> Can someone explain me the two observations?
> Francesco
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