[gmx-users] replica exchange

[rob yang]

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?

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
>MIME-Version: 1.0
>Received: from elvira.ekonomikum.uu.se ([130.238.164.5]) by 
>mc11-f23.hotmail.com with Microsoft SMTPSVC(6.0.3790.211); Tue, 1 Nov 2005 
>08:25:56 -0800
>Received: by elvira.ekonomikum.uu.se (Postfix, from userid 204)id 96C70401; 
>Tue,  1 Nov 2005 17:25:23 +0100 (MEZ)
>Received: from elvira.ekonomikum.uu.se(127.0.0.1) by 
>elvira.ekonomikum.uu.se via virus-scan id s26686; Tue, 1 Nov 05 17:25:12 
>+0100
>Received: from xray.bmc.uu.se (xray.bmc.uu.se [130.238.41.195])by 
>elvira.ekonomikum.uu.se (Postfix) with ESMTP id 4A2A53AC;Tue,  1 Nov 2005 
>17:25:12 +0100 (MEZ)
>Received: from xray.bmc.uu.se (localhost.localdomain [127.0.0.1])by 
>xray.bmc.uu.se (Postfix) with ESMTPid 55512251F9; Tue,  1 Nov 2005 17:25:10 
>+0100 (CET)
>Received: from colibri.its.uu.se (colibri.its.UU.SE [130.238.4.154])by 
>xray.bmc.uu.se (Postfix) with ESMTP id 5069E251F3for 
><gmx-users at gromacs.org>; Tue,  1 Nov 2005 17:25:08 +0100 (CET)
>Received: by colibri.its.uu.se (Postfix, from userid 211)id 32C11382; Tue,  
>1 Nov 2005 17:25:07 +0100 (NFT)
>Received: from colibri.its.uu.se(127.0.0.1) by colibri.its.uu.se 
>viavirus-scan id s14349; Tue, 1 Nov 05 17:25:00 +0100
>Received: from smtp1.rug.nl (smtp1.rug.nl [129.125.50.11])by 
>colibri.its.uu.se (Postfix) with SMTP id 09C77147for 
><gmx-users at gromacs.org>; Tue,  1 Nov 2005 17:24:59 +0100 (NFT)
>Received: from smtp1.rug.nl ([129.125.50.11])by smtp1.rug.nl (SMSSMTP 
>4.1.0.19) with SMTP id M2005110117210412519for <gmx-users at gromacs.org>; 
>Tue, 01 Nov 2005 17:21:04 +0100
>Received: from rug.nl (rugmd46.chem.rug.nl [129.125.42.46])by smtp1.rug.nl 
>(8.12.11/8.12.11) with ESMTP id jA1GL31I018305for <gmx-users at gromacs.org>; 
>Tue, 1 Nov 2005 17:21:04 +0100 (MET)
>X-Message-Info: sPHCaSLRLXzwLheB8L1nFLkwYeODjd+zXYMowYlfoXQ=
>X-Original-To: gmx-users at gromacs.org
>Delivered-To: gmx-users at xray.bmc.uu.se
>User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.6) Gecko/20040124
>X-Accept-Language: en-us, en
>References: <BAY104-F1784E718C93405DFB5611EC66F0 at phx.gbl>
>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: 01 Nov 2005 16:25:56.0983 (UTC) 
>FILETIME=[F005C070:01C5DF00]
>
>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
>----------------------------------
>
>_______________________________________________
>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.