[gmx-users] Re: gmx-users Digest, Vol 74, Issue 134
Carsten Kutzner
ckutzne at gwdg.de
Thu Jun 24 09:51:27 CEST 2010
Amin,
maybe your MPI-enabled executable is called mdrun_mpi. Check
the directory where mdrun is and make shure (with ldd for example)
the mdrun* you are using is linked to the MPI library you are using.
Carsten
On Jun 24, 2010, at 6:51 AM, Amin Arabbagheri wrote:
> 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
>
> ========================================
>
>
> ------------------------------
>
> --
> 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!
>
> End of gmx-users Digest, Vol 74, Issue 134
> ******************************************
>
> --
> 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!
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> www interface or send it to gmx-users-request at gromacs.org.
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--
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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