[gmx-users] Re: gmx-users Digest, Vol 85, Issue 19
Geethu Issac
geethumelody at gmail.com
Tue May 3 13:19:13 CEST 2011
Hello Mark.
yes i did check the link :) . but the error has been shown in the
ffgmxnb.itp file.I had received the itp file from sega and i modified it to
a topology file.
On Tue, May 3, 2011 at 7:20 PM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. Re: Invalid order for directive atomtypes (Mark Abraham)
> 2. Re: running job parallel (Mark Abraham)
> 3. Re: running job parallel (Bharati Singh)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 03 May 2011 20:00:43 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Invalid order for directive atomtypes
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DBFD24B.9030505 at anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On 3/05/2011 7:13 PM, Geethu Issac wrote:
> > Hello Users,
> >
> > I am a final year project student.I am doing simulation of gangliosdie
> > gm1 using gromacs 4.5.4. I am encountering an error in the energy
> > minimisation step(grompp -f ions.mdp -c gm1_solv.gro -p gm12.top -o
> > ions.tpr) saying
> >
> > *
> > -------------------------------------------------------
> > Program grompp, VERSION 4.5.4
> > Source code file: topio.c, line: 653
> >
> > Fatal error:
> > Syntax error - File ffgmxnb.itp, line 1
> > Last line read:
> > '[ atomtypes ]'
> > Invalid order for directive atomtypes
> > For more information and tips for troubleshooting, please check the
> > GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
> > *
> > The pdb file i have downloaded from 3DSDSCAR. I tried several times
> > with the same but am encountering the same error.Can anyone please
> > give me some guidelines or solution for the same.
>
> Did you follow that link and see what it has to say about this
> frequently-occurring problem?
>
> Mark
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> ------------------------------
>
> Message: 2
> Date: Tue, 03 May 2011 20:04:02 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] running job parallel
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DBFD312.7090709 at anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On 3/05/2011 7:37 PM, Bharati Singh wrote:
> > Hi Team,
> >
> > Thanks for your reply.
> >
> > I had tried following method to install gromacs-4.0.7 -
> >
> > $ module load intel_all/impi/default
> >
> > $ ./configure --enable-mpi --with-fft=fftw2
> > LDFLAGS="-L/sfs1/lib/sfftw-2.1.5/lib/"
> > CPPFLAGS="-I/sfs1/lib/sfftw-2.1.5/include" LIBS="-lsfftw" F77=mpif77
> > --prefix=/sfs3/home/bharati/gromacs
> >
> > $ make
> > $ make install
> >
> > Following the command to submit the job in queue:
> >
> > bsub -q normal4c -n 4 mpirun -srun
> > /sfs3/home/bharati/gromacs/bin/mdrun -pd -v -s Ag6A12_equil.tpr -o
> > Ag6A12_equil.trr -c Ag6A12_equil.gro -e Ag6A12_equil.edr -g
> > Ag6A12_equil.log
> >
> >
> > When I submit the job for more than one processors in queue, it gets
> > terminated immediately without error. It is not creating any file etc..
>
> That set of commands should create mdrun_mpi. Why are you not using it?
>
> If this mdrun really is the one produced by the above configuration, the
> symptoms suggest some kind of (dynamic) linking problem, but we have no
> way to be more specific. It's not GROMACS-related.
>
> Mark
>
> >
> > Thanks & Regards,
> >
> > On Tue, May 3, 2011 at 2:40 PM, Saikat Banerjee
> > <banskt.saikat at gmail.com <mailto:banskt.saikat at gmail.com>> wrote:
> >
> > Hi,
> >
> > Have you checked the error log? Please post the error log.
> >
> > Have you configured GROMACS using --enable-mpi?
> >
> > Thanks,
> > Saikat
> >
> > On Tue, May 3, 2011 at 2:35 PM, Bharati Singh
> > <bharati0307 at gmail.com <mailto:bharati0307 at gmail.com>> wrote:
> >
> > Hi Team,
> >
> > I have LSF in my cluster ,I have installed gromacs-4.0.7 on
> > Sampige. It is working fine as a serial(on 1 processor) ,when
> > I submit the job for more than one processors in queue, it
> > gets terminated immediately.Can you suggest me something about
> > it, please
> >
> > Thanks & Regards,
> >
> > --
> > Bharati Singh
> > System Administrator
> > Centre for Computational Materials Science(CCMS)
> > Jawaharlal Nehru Centre for Advanced Scientific Research(JNCASR),
> > Bangalore - 560 064
> > India.
> > mob. : 08970898515
> > Phone : +91 80 2208 2944 + Ext. 26 & 28
> > Fax : +91 80 2208 2906
> > Email : bharati_singh at jncasr.ac.in <mailto:amit at jncasr.ac.in>
> >
> >
> > http://www.jncasr.ac.in/ccms
> > http://www.jncasr.ac.in/
> >
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > <mailto:gmx-users at gromacs.org>
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/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
> > <mailto:gmx-users-request at gromacs.org>.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> >
> >
> >
> > --
> > -------------------------------------------------------------------
> > Saikat Banerjee
> > Integrated Ph.D student
> > Prof B. Bagchi's group
> > Room no. 210
> > Solid State and Structural Chemistry Unit (SSCU)
> > Indian Institute of Science
> > Bangalore-560012
> >
> > Ph: +91-80-22933305 (lab)
> > +91-80-23602338 (lab)
> > +91-9980228606 (mobile)
> >
> > Alternate e-mail:
> > saikat at sscu.iisc.ernet.in <mailto:saikat at sscu.iisc.ernet.in>
> > banskt at yahoo.co.in <mailto:banskt at yahoo.co.in>
> > -------------------------------------------------------------------
> >
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > <mailto:gmx-users at gromacs.org>
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/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
> > <mailto:gmx-users-request at gromacs.org>.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> >
> >
> >
> > --
> > Bharati Singh
> > System Administrator
> > Centre for Computational Materials Science(CCMS)
> > Jawaharlal Nehru Centre for Advanced Scientific Research(JNCASR),
> > Bangalore - 560 064
> > India.
> > mob. : 08970898515
> > Phone : +91 80 2208 2944 + Ext. 26 & 28
> > Fax : +91 80 2208 2906
> > Email : bharati_singh at jncasr.ac.in <mailto:amit at jncasr.ac.in>
> >
> >
> > http://www.jncasr.ac.in/ccms
> > http://www.jncasr.ac.in/
>
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> ------------------------------
>
> Message: 3
> Date: Tue, 3 May 2011 15:49:47 +0530
> From: Bharati Singh <bharati0307 at gmail.com>
> Subject: Re: [gmx-users] running job parallel
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <BANLkTinW1Lu-oZqV=bYfcB32sBuyBo=r9g at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Mentioned method is working in another user's home directory on same
> machine, then I dont think the problem with linking.
>
>
>
> On Tue, May 3, 2011 at 3:34 PM, Mark Abraham <Mark.Abromeaham at anu.edu.au
> >wrote:
>
> > On 3/05/2011 7:37 PM, Bharati Singh wrote:
> >
> > Hi Team,
> >
> > Thanks for your reply.
> >
> > I had tried following method to install gromacs-4.0.7 -
> >
> > $ module load intel_all/impi/default
> >
> > $ ./configure --enable-mpi --with-fft=fftw2
> > LDFLAGS="-L/sfs1/lib/sfftw-2.1.5/lib/"
> > CPPFLAGS="-I/sfs1/lib/sfftw-2.1.5/include" LIBS="-lsfftw" F77=mpif77
> > --prefix=/sfs3/home/bharati/gromacs
> >
> > $ make
> > $ make install
> >
> > Following the command to submit the job in queue:
> >
> > bsub -q normal4c -n 4 mpirun -srun /sfs3/home/bharati/gromacs/bin/mdrun
> > -pd -v -s Ag6A12_equil.tpr -o Ag6A12_equil.trr -c Ag6A12_equil.gro -e
> > Ag6A12_equil.edr -g Ag6A12_equil.log
> >
> >
> > When I submit the job for more than one processors in queue, it gets
> > terminated immediately without error. It is not creating any file etc..
> >
> >
> > That set of commands should create mdrun_mpi. Why are you not using it?
> >
> > If this mdrun really is the one produced by the above configuration, the
> > symptoms suggest some kind of (dynamic) linking problem, but we have no
> way
> > to be more specific. It's not GROMACS-related.
> >
> > Mark
> >
> >
> >
> > Thanks & Regards,
> >
> > On Tue, May 3, 2011 at 2:40 PM, Saikat Banerjee <banskt.saikat at gmail.com
> >wrote:
> >
> >> Hi,
> >>
> >> Have you checked the error log? Please post the error log.
> >>
> >> Have you configured GROMACS using --enable-mpi?
> >>
> >> Thanks,
> >> Saikat
> >>
> >> On Tue, May 3, 2011 at 2:35 PM, Bharati Singh <bharati0307 at gmail.com
> >wrote:
> >>
> >>> Hi Team,
> >>>
> >>> I have LSF in my cluster ,I have installed gromacs-4.0.7 on Sampige. It
> >>> is working fine as a serial(on 1 processor) ,when I submit the job for
> >>> more than one processors in queue, it gets terminated immediately.Can
> you
> >>> suggest me something about it, please
> >>>
> >>> Thanks & Regards,
> >>>
> >>> --
> >>> Bharati Singh
> >>> System Administrator
> >>> Centre for Computational Materials Science(CCMS)
> >>> Jawaharlal Nehru Centre for Advanced Scientific Research(JNCASR),
> >>> Bangalore - 560 064
> >>> India.
> >>> mob. : 08970898515
> >>> Phone : +91 80 2208 2944 + Ext. 26 & 28
> >>> Fax : +91 80 2208 2906
> >>> Email : bharati_singh at jncasr.ac.in <amit at jncasr.ac.in>
> >>>
> >>>
> >>> http://www.jncasr.ac.in/ccms
> >>> http://www.jncasr.ac.in/
> >>>
> >>> --
> >>> 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/Support/Mailing_Lists/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/Support/Mailing_Lists
> >>>
> >>
> >>
> >>
> >> --
> >> -------------------------------------------------------------------
> >> Saikat Banerjee
> >> Integrated Ph.D student
> >> Prof B. Bagchi's group
> >> Room no. 210
> >> Solid State and Structural Chemistry Unit (SSCU)
> >> Indian Institute of Science
> >> Bangalore-560012
> >>
> >> Ph: +91-80-22933305 (lab)
> >> +91-80-23602338 (lab)
> >> +91-9980228606 (mobile)
> >>
> >> Alternate e-mail:
> >> saikat at sscu.iisc.ernet.in
> >> banskt at yahoo.co.in
> >> -------------------------------------------------------------------
> >>
> >> --
> >> 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/Support/Mailing_Lists/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/Support/Mailing_Lists
> >>
> >
> >
> >
> > --
> > Bharati Singh
> > System Administrator
> > Centre for Computational Materials Science(CCMS)
> > Jawaharlal Nehru Centre for Advanced Scientific Research(JNCASR),
> > Bangalore - 560 064
> > India.
> > mob. : 08970898515
> > Phone : +91 80 2208 2944 + Ext. 26 & 28
> > Fax : +91 80 2208 2906
> > Email : bharati_singh at jncasr.ac.in <amit at jncasr.ac.in>
> >
> >
> > http://www.jncasr.ac.in/ccms
> > http://www.jncasr.ac.in/
> >
> >
> >
> > --
> > 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/Support/Mailing_Lists/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/Support/Mailing_Lists
> >
>
>
>
> --
> Bharati Singh
> System Administrator
> Centre for Computational Materials Science(CCMS)
> Jawaharlal Nehru Centre for Advanced Scientific Research(JNCASR),
> Bangalore - 560 064
> India.
> mob. : 08970898515
> Phone : +91 80 2208 2944 + Ext. 26 & 28
> Fax : +91 80 2208 2906
> Email : bharati_singh at jncasr.ac.in <amit at jncasr.ac.in>
>
>
> http://www.jncasr.ac.in/ccms
> http://www.jncasr.ac.in/
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>
> End of gmx-users Digest, Vol 85, Issue 19
> *****************************************
>
--
*Geethu Issac*
*
"A life spent making mistakes is not only more honorable, but more useful
than a life spent doing nothing."
-George Bernard Shaw*
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