[gmx-users] Drift and crash

[BON Michael]

Hi,

I have been struggling for more than one month with a permanent problem in my simulations. I asked about it in previous mails in this mailing-list. Briefly, the problem is that my simulations crash at some point, and there is nothing explaining it. Nothing but a strange behaviour spotted in msd plot (with g_msd) which show that the motion is somewhat discontinuous, whereas the energies, pressure, temperature are perfectly OK.
Recently, I tried this : I ran the files of water simulation of the tutorial (water directory), except I change nsteps = 10000 for nsteps = 1000000 in the grompp.mdp file. That's the only change I made.

And the simulation crashed quickly, for the same reasons.

Could anyone try to run this simulation on his computer and tell me whether it works. I really don't understand what is going on.

I am using a PowerBookG4, gromacs 3.3.1, my parameters of configuration are : 
 --enable-shared --prefix=%p --exec-prefix=%p --mandir=%p/share --with-external_lapack --with-external_blas

Thanks,
Michael Bon
michael.bon at cea.fr


-------- Message d'origine--------
De: gmx-users-bounces at gromacs.org de la part de gmx-users-request at gromacs.org
Date: jeu. 27/09/2007 12:00
À: gmx-users at gromacs.org
Objet : gmx-users Digest, Vol 41, Issue 88
 
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Today's Topics:

   1. how to remove periodicity when using g_rmsd (TANG JIAOWEI)
   2. Re: how to remove periodicity when using g_rmsd (Florian Haberl)


----------------------------------------------------------------------

Message: 1
Date: Thu, 27 Sep 2007 11:29:59 +0200
From: "TANG JIAOWEI" <tangxuan82 at gmail.com>
Subject: [gmx-users] how to remove periodicity when using g_rmsd
To: gmx-users at gromacs.org
Message-ID:
	<29a72e3b0709270229o18ad302djdd90d5fd853ba797 at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Dear all,
I am studying on a big protein with 16 subunits and when i used g_rmsd to
one subunit of the protein, the result seems strange that the structure of
the subunit changes much but it should not.. I searched the mailing list and
it may be caused by the periodic thing. Could you tell me how to remove the
periodic thing in detail before i use g_rmsd.

Thank you

Tang jiaowei
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Message: 2
Date: Thu, 27 Sep 2007 11:40:53 +0200
From: Florian Haberl <Florian.Haberl at chemie.uni-erlangen.de>
Subject: Re: [gmx-users] how to remove periodicity when using g_rmsd
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <200709271140.54914.Florian.Haberl at chemie.uni-erlangen.de>
Content-Type: text/plain;  charset="utf-8"

Hi,
On Thursday, 27. September 2007 11:29, TANG JIAOWEI wrote:
> Dear all,
> I am studying on a big protein with 16 subunits and when i used g_rmsd to
> one subunit of the protein, the result seems strange that the structure of
> the subunit changes much but it should not.. I searched the mailing list
> and it may be caused by the periodic thing. Could you tell me how to remove
> the periodic thing in detail before i use g_rmsd.

something like:

trjconv -s yourmdstartfile.tpr -f yourtrj.trr -o pbc.trr -pbc nojump

select as group your complete system.

than g_rmsd ...

>
> Thank you
>
> Tang jiaowei


Greetings,

Florian

-- 
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 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone:  	+49(0) â^' 9131 â^' 85 26581
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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