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. Best, Michael On Thu, May 10, 2012 at 12:23 PM, francesco oteri <francesco.ot...@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 > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
