[gmx-users] replica exchange

David spoel at xray.bmc.uu.se
Fri Nov 4 08:25:21 CET 2005


On Thu, 2005-11-03 at 17:16 -0600, rob yang wrote:
> More questions. Thank you all for helping me along.
> 1) I've been doing NPT REMD. Just outta curiocity, can you do NVT using 
> gromacs?
Sure, just turn off pressure coupling in your mdp files.

> 2) I've only been able to observe swaps by neighbouring runs.  Is it 
> possible at all for non-adjacent runs to swap if their energy is close 
> enough? The reason why I am asking is because I am playing with the spacing 
> and hence minimal number of parallel runs I need for my system.
It is not implemented for the reason that in most cases the
probabilities would be vanishingly small.

> 
> Thank you
> 
> rob
> 
> 
> >From: David <spoel at xray.bmc.uu.se>
> >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: Thu, 03 Nov 2005 18:47:39 +0100
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> >
> >On Thu, 2005-11-03 at 10:10 -0600, rob yang wrote:
> > > hello again,
> > > still hacking away at RE. so i got it to run for a while and then it 
> >died
> > > with the message:
> > > -------------------------------------------------------
> > > Program mdrun_mpi, VERSION 3.3
> > > Source code file: enxio.c, line: 343
> > >
> > > Fatal error:
> > > could not write energies
> > > -------------------------------------------------------
> > > is this a memory related error?
> >disk full?
> >
> > >
> > > also, is there a pre-defined waiting length for the different runs to
> > > finish? ie, if i am running 2 jobs on 2 diff machines and 1 of them 
> >finishes
> > > way earlier than the other, does the program sit idle for X seconds 
> >waiting
> > > for job2  and terminates if the wait is longer than X seconds? if so, is
> > > there a parameter to set X ourselves?
> >
> >I think something like this was fixed sometime ago...
> >Otherwise check whether your sims are in sync.
> >
> > >
> > > thanks alot.
> > >
> > > rob
> > >
> > >
> > > _______________________________________________
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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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> 
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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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