[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
> >MIME-Version: 1.0
> >Received: from elvira.ekonomikum.uu.se ([130.238.164.5]) by 
> >MC8-F42.hotmail.com with Microsoft SMTPSVC(6.0.3790.211); Thu, 3 Nov 2005 
> >09:51:51 -0800
> >Received: by elvira.ekonomikum.uu.se (Postfix, from userid 204)id D03CF1D0; 
> >Thu,  3 Nov 2005 18:51:49 +0100 (MEZ)
> >Received: from elvira.ekonomikum.uu.se(127.0.0.1) by 
> >elvira.ekonomikum.uu.se via virus-scan id s26740; Thu, 3 Nov 05 18:51:40 
> >+0100
> >Received: from xray.bmc.uu.se (xray.bmc.uu.se [130.238.41.195])by 
> >elvira.ekonomikum.uu.se (Postfix) with ESMTP id DD33D3F3;Thu,  3 Nov 2005 
> >18:51:39 +0100 (MEZ)
> >Received: from xray.bmc.uu.se (localhost.localdomain [127.0.0.1])by 
> >xray.bmc.uu.se (Postfix) with ESMTPid 2107425083; Thu,  3 Nov 2005 18:51:39 
> >+0100 (CET)
> >Received: from elvira.ekonomikum.uu.se 
> >(elvira.ekonomikum.uu.se[130.238.164.5]) by xray.bmc.uu.se (Postfix) with 
> >ESMTP id D930125083for <gmx-users at gromacs.org>; Thu,  3 Nov 2005 18:51:34 
> >+0100 (CET)
> >Received: by elvira.ekonomikum.uu.se (Postfix, from userid 204)id BEBE31D0; 
> >Thu,  3 Nov 2005 18:51:34 +0100 (MEZ)
> >Received: from elvira.ekonomikum.uu.se(127.0.0.1) by 
> >elvira.ekonomikum.uu.sevia virus-scan id s26633; Thu, 3 Nov 05 18:51:24 
> >+0100
> >Received: from 
> >pne-smtpout1-sn1.fre.skanova.net(pne-smtpout1-sn1.fre.skanova.net 
> >[81.228.11.98])by elvira.ekonomikum.uu.se (Postfix) with ESMTP id 
> >5D97B4ECfor <gmx-users at gromacs.org>; Thu,  3 Nov 2005 18:51:24 +0100 (MEZ)
> >Received: from 217-208-143-88-o1123.tbon.telia.com (217.208.143.88) 
> >bypne-smtpout1-sn1.fre.skanova.net (7.2.060.1)id 4368D4B90005DFA5 for 
> >gmx-users at gromacs.org;Thu, 3 Nov 2005 18:47:39 +0100
> >X-Message-Info: o8IIVuzO8A3arfnntax85zFnPdRTLJ9CCZratKvu7PY=
> >X-Original-To: gmx-users at gromacs.org
> >Delivered-To: gmx-users at xray.bmc.uu.se
> >References: <BAY104-F1968EB0E4B37656E63CDE8C6610 at phx.gbl>
> >X-Mailer: Evolution 2.0.4 (2.0.4-7) X-BeenThere: gmx-users at gromacs.org
> >X-Mailman-Version: 2.1.4
> >Precedence: list
> >List-Id: Discussion list for GROMACS users <gmx-users.gromacs.org>
> >List-Unsubscribe: 
> ><http://www.gromacs.org/mailman/listinfo/gmx-users>,<mailto:gmx-users-request at gromacs.org?subject=unsubscribe>
> >List-Archive: <http://www.gromacs.org/pipermail/gmx-users>
> >List-Post: <mailto:gmx-users at gromacs.org>
> >List-Help: <mailto:gmx-users-request at gromacs.org?subject=help>
> >List-Subscribe: 
> ><http://www.gromacs.org/mailman/listinfo/gmx-users>,<mailto:gmx-users-request at gromacs.org?subject=subscribe>
> >Errors-To: gmx-users-bounces at gromacs.org
> >Return-Path: gmx-users-bounces at gromacs.org
> >X-OriginalArrivalTime: 03 Nov 2005 17:51:52.0842 (UTC) 
> >FILETIME=[45FAE6A0:01C5E09F]
> >
> >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
> > >
> > >
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> >--
> >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
> >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> >_______________________________________________
> >gmx-users mailing list
> >gmx-users at gromacs.org
> >http://www.gromacs.org/mailman/listinfo/gmx-users
> >Please don't post (un)subscribe requests to the list. Use the
> >www interface or send it to gmx-users-request at gromacs.org.
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

More information about the gromacs.org_gmx-users mailing list