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, <[email protected]> wrote: > Send gmx-users mailing list submissions to > [email protected] > > 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 > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > 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 <[email protected]> > Subject: Re: [gmx-users] Invalid order for directive atomtypes > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110503/b7c66e58/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Tue, 03 May 2011 20:04:02 +1000 > From: Mark Abraham <[email protected]> > Subject: Re: [gmx-users] running job parallel > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > 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 > > <[email protected] <mailto:[email protected]>> 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 > > <[email protected] <mailto:[email protected]>> 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 : [email protected] <mailto:[email protected]> > > > > > > http://www.jncasr.ac.in/ccms > > http://www.jncasr.ac.in/ > > > > -- > > gmx-users mailing list [email protected] > > <mailto:[email protected]> > > 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 [email protected] > > <mailto:[email protected]>. > > 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: > > [email protected] <mailto:[email protected]> > > [email protected] <mailto:[email protected]> > > ------------------------------------------------------------------- > > > > -- > > gmx-users mailing list [email protected] > > <mailto:[email protected]> > > 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 [email protected] > > <mailto:[email protected]>. > > 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 : [email protected] <mailto:[email protected]> > > > > > > http://www.jncasr.ac.in/ccms > > http://www.jncasr.ac.in/ > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110503/609b5aaf/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Tue, 3 May 2011 15:49:47 +0530 > From: Bharati Singh <[email protected]> > Subject: Re: [gmx-users] running job parallel > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > 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 <[email protected] > >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 <[email protected] > >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 <[email protected] > >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 : [email protected] <[email protected]> > >>> > >>> > >>> http://www.jncasr.ac.in/ccms > >>> http://www.jncasr.ac.in/ > >>> > >>> -- > >>> gmx-users mailing list [email protected] > >>> 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 [email protected]. > >>> 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: > >> [email protected] > >> [email protected] > >> ------------------------------------------------------------------- > >> > >> -- > >> gmx-users mailing list [email protected] > >> 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 [email protected]. > >> 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 : [email protected] <[email protected]> > > > > > > http://www.jncasr.ac.in/ccms > > http://www.jncasr.ac.in/ > > > > > > > > -- > > gmx-users mailing list [email protected] > > 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 [email protected]. > > 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 : [email protected] <[email protected]> > > > http://www.jncasr.ac.in/ccms > http://www.jncasr.ac.in/ > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110503/85418614/attachment.html > > ------------------------------ > > -- > gmx-users mailing list > [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > 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*
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
