[gmx-users] replica exchange

[rob yang]

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?
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.

Thank you

rob


>From: David <spoel at xray.bmc.uu.se>
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>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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