[gmx-users] replica exchange
David van der Spoel
spoel at xray.bmc.uu.se
Wed Nov 2 10:40:15 CET 2005
On Tue, 2005-11-01 at 15:58 -0600, rob yang wrote:
> 1 more quick q:
> mpirun -np 2 mdrun_mpi -s input.tpr -np 2 -replex 1000
> do I need a -multi flag here? i've seen people using -multi flag but I can
> get it to run without it so what gives?
no/
>
> thank you
>
> rob
>
>
> >From: Xavier Periole <x.periole at rug.nl>
> >Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >Subject: Re: [gmx-users] replica exchange
> >Date: Tue, 01 Nov 2005 17:20:11 +0100
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> >
> >rob yang wrote:
> >
> >>Hi gmxers,
> >>I have a general question about the implementation behind RE in 3.3. if I
> >>were to run the following command:
> >>mpirun -np 2 mdrun_mpi -s input.tpr -np 2 -replex 1000
> >>
> >>where there are 2 .tpr files already made in the directory: input0.tpr,
> >>input1.tpr
> >>and I have defined 2 independent computers linked by network.
> >>
> >>would gromacs run the two sim independently on the two computers and only
> >>communicate with each other every 1000 steps? or
> >>would gromacs try to run 1 sim parallelly on both computers first and then
> >>the other? ie: constant communication between the 2 computers through
> >>network which would definately be slower.
> >
> >first case.
> >
> >>
> >>In case the above command makes no sense, here's what I want to do:
> >>given two sims differred only by the temperature, I'd like to run RE using
> >>two boxes with the swapping rate being every 1000 steps. Ideally, I'd like
> >>to have one sim per box, which only talks to each other at the swapping
> >>time.
> >>
> >>p.s. another q on how to analyze the results. Should I concat input0.trr
> >>and input1.trr into a single file at the end of the run? Or treat them as
> >>two separate and independent runs?
> >>
> >That is your choice !! Depend on what your are interested in !! And mixing
> >temperatures is not generally
> >what is interesting. One advantages of REMD is to generate properties over
> >a range of temperatures...
> >
> >>thank you very much in advance.
> >>
> >>rob
> >
> >XAvier
> >
> >--
> >----------------------------------
> >Xavier Periole - Ph.D.
> >
> >Dept. of Biophysical Chemistry / MD Group Univ. of Groningen
> >Nijenborgh 4
> >9747 AG Groningen
> >The Netherlands
> >
> >Tel: +31-503634329
> >Fax: +31-503634800
> >email: x.periole at rug.nl
> >web-page: http://md.chem.rug.nl/~periole
> >----------------------------------
> >
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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