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-requ...@gromacs.org > <gmx-users-requ...@gromacs.org> wrote: > > From: gmx-users-requ...@gromacs.org <gmx-users-requ...@gromacs.org> > Subject: gmx-users Digest, Vol 74, Issue 134 > To: gmx-users@gromacs.org > Date: Monday, 21 June, 2010, 9:03 > > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > 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_a...@yahoo.com> > Subject: [gmx-users] (no subject) > To: gmx-users@gromacs.org > Message-ID: <180446.74209...@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 > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100621/fd800779/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Mon, 21 Jun 2010 08:05:15 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] (no subject) > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4c1f557b.4090...@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 <bio...@talavis.eu> > Subject: Re: [gmx-users] (no subject) > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <aanlktilfhuno5zfxqismsuvestyfq-igiorzujmcr...@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_a...@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@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-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100621/ccd8a2ba/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Mon, 21 Jun 2010 14:07:50 +0200 > From: Carsten Kutzner <ckut...@gwdg.de> > Subject: Re: [gmx-users] (no subject) > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <313e9026-5663-4013-a601-b5973ec89...@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@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-requ...@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 > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100621/fc58c68a/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Mon, 21 Jun 2010 05:58:31 -0700 (PDT) > From: Omololu Akin-Ojo <prayerz4us...@yahoo.com> > Subject: [gmx-users] Help with defining new residue (OXY--HEME) > To: gmx-users@gromacs.org > Message-ID: <633186.76002...@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. > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100621/b001dbd1/attachment-0001.html > > ------------------------------ > > Message: 6 > Date: Mon, 21 Jun 2010 09:02:06 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] Help with defining new residue (OXY--HEME) > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4c1f62ce.2030...@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@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@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-requ...@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
-- gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php