[gmx-users] Re: gmx-users Digest, Vol 74, Issue 134
Amin Arabbagheri
amin_arab at yahoo.com
Thu Jun 24 06:51:00 CEST 2010
Carsten,
Thanks for your help, I used something like "mpirun -np 3 mdrun -s topol.tpr",
it works but its something like repeating a single job 3 times, simultaneously.
here is the output on the screen :
{
Back Off! I just backed up md_traj_dam_2nd.trr to ./#md_traj_dam_2nd.trr.1#
Back Off! I just backed up ener.edr to ./#ener.edr.1#
Back Off! I just backed up md_traj_dam_2nd.trr to ./#md_traj_dam_2nd.trr.2#
Back Off! I just backed up ener.edr to ./#ener.edr.2#
Back Off! I just backed up md_traj_dam_2nd.trr to ./#md_traj_dam_2nd.trr.3#
Back Off! I just backed up ener.edr to ./#ener.edr.3#
starting mdrun 'Protein in water'
1000000 steps, 1000.0 ps.
starting mdrun 'Protein in water'
1000000 steps, 1000.0 ps.
starting mdrun 'Protein in water'
1000000 steps, 1000.0 ps.
step 736900, will finish Fri Jun 25 07:45:04 2010
}
the estimated time is as long as one single job!
--- On Mon, 21/6/10, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org> wrote:
From: gmx-users-request at gromacs.org <gmx-users-request at gromacs.org>
Subject: gmx-users Digest, Vol 74, Issue 134
To: gmx-users at gromacs.org
Date: Monday, 21 June, 2010, 9:03
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Today's Topics:
1. (no subject) (Amin Arabbagheri)
2. Re: (no subject) (Justin A. Lemkul)
3. Re: (no subject) (Linus ?stberg)
4. Re: (no subject) (Carsten Kutzner)
5. Help with defining new residue (OXY--HEME) (Omololu Akin-Ojo)
6. Re: Help with defining new residue (OXY--HEME) (Justin A. Lemkul)
----------------------------------------------------------------------
Message: 1
Date: Mon, 21 Jun 2010 05:00:04 -0700 (PDT)
From: Amin Arabbagheri <amin_arab at yahoo.com>
Subject: [gmx-users] (no subject)
To: gmx-users at gromacs.org
Message-ID: <180446.74209.qm at web50607.mail.re2.yahoo.com>
Content-Type: text/plain; charset="utf-8"
Hi all,
I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic package manager.
I want to run a simulation in parallel on a multi processor, single PC, but to compile via grompp, it doesn't accept -np flag, and also , using -np in mdrun, it still runs as a single job.
Thanks a lot for any instruction.
Bests,
Amin
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Message: 2
Date: Mon, 21 Jun 2010 08:05:15 -0400
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] (no subject)
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4C1F557B.4090102 at vt.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed
Amin Arabbagheri wrote:
> Hi all,
>
> I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic
> package manager.
> I want to run a simulation in parallel on a multi processor, single PC,
> but to compile via grompp, it doesn't accept -np flag, and also , using
> -np in mdrun, it still runs as a single job.
> Thanks a lot for any instruction.
>
Regarding grompp:
http://www.gromacs.org/Documentation/FAQs
As for mdrun, please provide your actual command line. The mdrun -np flag is
nonfunctional, instead the number of nodes are taken from, i.e. mpirun -np from
which mdrun is launched.
-Justin
> Bests,
> Amin
>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 3
Date: Mon, 21 Jun 2010 14:07:54 +0200
From: Linus ?stberg <bioinf at talavis.eu>
Subject: Re: [gmx-users] (no subject)
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
<AANLkTilFHUNo5ZfXQISmSUvesTYfQ-iGioRZuJmCr1LG at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Use grompp normally, without the -np flag. Then run mdrun_mpi with your
normal parameters as mpirun -np x mdrun_mpi -deffnm xx
On Mon, Jun 21, 2010 at 2:00 PM, Amin Arabbagheri <amin_arab at yahoo.com>wrote:
> Hi all,
>
> I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic
> package manager.
> I want to run a simulation in parallel on a multi processor, single PC, but
> to compile via grompp, it doesn't accept -np flag, and also , using -np in
> mdrun, it still runs as a single job.
> Thanks a lot for any instruction.
>
> Bests,
> Amin
>
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
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Message: 4
Date: Mon, 21 Jun 2010 14:07:50 +0200
From: Carsten Kutzner <ckutzne at gwdg.de>
Subject: Re: [gmx-users] (no subject)
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <313E9026-5663-4013-A601-B5973EC89D94 at gwdg.de>
Content-Type: text/plain; charset="us-ascii"
Amin,
the -np flag is not necessary any more for grompp in Gromacs 4.0.
For mdrun, just use something like
mpirun -np 4 mdrun -s topol.tpr
Carsten
On Jun 21, 2010, at 2:00 PM, Amin Arabbagheri wrote:
> Hi all,
>
> I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic package manager.
> I want to run a simulation in parallel on a multi processor, single PC, but to compile via grompp, it doesn't accept -np flag, and also , using -np in mdrun, it still runs as a single job.
> Thanks a lot for any instruction.
>
> Bests,
> Amin
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
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Message: 5
Date: Mon, 21 Jun 2010 05:58:31 -0700 (PDT)
From: Omololu Akin-Ojo <prayerz4users at yahoo.com>
Subject: [gmx-users] Help with defining new residue (OXY--HEME)
To: gmx-users at gromacs.org
Message-ID: <633186.76002.qm at web58608.mail.re3.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
I obtained parameters for a Morse potential between Oxygen molecule and Iron in heme (from ab initio calculations). How can I use this potential with the GROMOS96 parameters?
I thought of a couple of options:
1) Define a new residue -- OXYHEM using the same parameters for HEME as in ffG43a1.rtp but just adding oxygen--heme interaction.
(The problem with this is that the bonded interaction in the HEME uses the G96BOND, so, how would I maintain this G96BOND for all the atoms except the oxygen-Fe interaction for which I need to use the Morse potential).
** What are the steps needed to do this? ***
2. Is it possible to simply create an appropriate *.itp file to use in conjunction with the HEME already defined in the GROMOS96 files (*.atp, *.itp, *.rtp in /usr/local/gromacs/share/gromacs/top)?
Any help will be appreciated.
Thanks.
o.
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Message: 6
Date: Mon, 21 Jun 2010 09:02:06 -0400
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] Help with defining new residue (OXY--HEME)
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4C1F62CE.2030503 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Omololu Akin-Ojo wrote:
> Hi,
>
> I obtained parameters for a Morse potential between Oxygen molecule and
> Iron in heme (from ab initio calculations). How can I use this
> potential with the GROMOS96 parameters?
>
> I thought of a couple of options:
>
> 1) Define a new residue -- OXYHEM using the same parameters for HEME as
> in ffG43a1.rtp but just adding oxygen--heme interaction.
> (The problem with this is that the bonded interaction in the HEME uses
> the G96BOND, so, how would I maintain this G96BOND for all the atoms
> except the oxygen-Fe interaction for which I need to use the Morse
> potential).
> ** What are the steps needed to do this? ***
>
You could create an .rtp entry for this species and process it with pdb2gmx. I
don't know how to put a Morse type bond in an .rtp file, but you can easily
modify the resulting topology to include the proper term.
> 2. Is it possible to simply create an appropriate *.itp file to use in
> conjunction with the HEME already defined in the GROMOS96 files (*.atp,
> *.itp, *.rtp in /usr/local/gromacs/share/gromacs/top)?
>
Sure, most things are possible :) See the manual, chapter 5.
-Justin
> Any help will be appreciated.
>
> Thanks.
>
> o.
>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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