Hello Mark.<br><br>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.<br><br><div class="gmail_quote">On Tue, May 3, 2011 at 7:20 PM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br>
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Today's Topics:<br>
<br>
1. Re: Invalid order for directive atomtypes (Mark Abraham)<br>
2. Re: running job parallel (Mark Abraham)<br>
3. Re: running job parallel (Bharati Singh)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 03 May 2011 20:00:43 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] Invalid order for directive atomtypes<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4DBFD24B.9030505@anu.edu.au">4DBFD24B.9030505@anu.edu.au</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
On 3/05/2011 7:13 PM, Geethu Issac wrote:<br>
> Hello Users,<br>
><br>
> I am a final year project student.I am doing simulation of gangliosdie<br>
> gm1 using gromacs 4.5.4. I am encountering an error in the energy<br>
> minimisation step(grompp -f ions.mdp -c gm1_solv.gro -p gm12.top -o<br>
> ions.tpr) saying<br>
><br>
> *<br>
> -------------------------------------------------------<br>
> Program grompp, VERSION 4.5.4<br>
> Source code file: topio.c, line: 653<br>
><br>
> Fatal error:<br>
> Syntax error - File ffgmxnb.itp, line 1<br>
> Last line read:<br>
> '[ atomtypes ]'<br>
> Invalid order for directive atomtypes<br>
> For more information and tips for troubleshooting, please check the<br>
> GROMACS<br>
> website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
> -------------------------------------------------------<br>
> *<br>
> The pdb file i have downloaded from 3DSDSCAR. I tried several times<br>
> with the same but am encountering the same error.Can anyone please<br>
> give me some guidelines or solution for the same.<br>
<br>
Did you follow that link and see what it has to say about this<br>
frequently-occurring problem?<br>
<br>
Mark<br>
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Message: 2<br>
Date: Tue, 03 May 2011 20:04:02 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] running job parallel<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4DBFD312.7090709@anu.edu.au">4DBFD312.7090709@anu.edu.au</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
On 3/05/2011 7:37 PM, Bharati Singh wrote:<br>
> Hi Team,<br>
><br>
> Thanks for your reply.<br>
><br>
> I had tried following method to install gromacs-4.0.7 -<br>
><br>
> $ module load intel_all/impi/default<br>
><br>
> $ ./configure --enable-mpi --with-fft=fftw2<br>
> LDFLAGS="-L/sfs1/lib/sfftw-2.1.5/lib/"<br>
> CPPFLAGS="-I/sfs1/lib/sfftw-2.1.5/include" LIBS="-lsfftw" F77=mpif77<br>
> --prefix=/sfs3/home/bharati/gromacs<br>
><br>
> $ make<br>
> $ make install<br>
><br>
> Following the command to submit the job in queue:<br>
><br>
> bsub -q normal4c -n 4 mpirun -srun<br>
> /sfs3/home/bharati/gromacs/bin/mdrun -pd -v -s Ag6A12_equil.tpr -o<br>
> Ag6A12_equil.trr -c Ag6A12_equil.gro -e Ag6A12_equil.edr -g<br>
> Ag6A12_equil.log<br>
><br>
><br>
> When I submit the job for more than one processors in queue, it gets<br>
> terminated immediately without error. It is not creating any file etc..<br>
<br>
That set of commands should create mdrun_mpi. Why are you not using it?<br>
<br>
If this mdrun really is the one produced by the above configuration, the<br>
symptoms suggest some kind of (dynamic) linking problem, but we have no<br>
way to be more specific. It's not GROMACS-related.<br>
<br>
Mark<br>
<br>
><br>
> Thanks & Regards,<br>
><br>
> On Tue, May 3, 2011 at 2:40 PM, Saikat Banerjee<br>
> <<a href="mailto:banskt.saikat@gmail.com">banskt.saikat@gmail.com</a> <mailto:<a href="mailto:banskt.saikat@gmail.com">banskt.saikat@gmail.com</a>>> wrote:<br>
><br>
> Hi,<br>
><br>
> Have you checked the error log? Please post the error log.<br>
><br>
> Have you configured GROMACS using --enable-mpi?<br>
><br>
> Thanks,<br>
> Saikat<br>
><br>
> On Tue, May 3, 2011 at 2:35 PM, Bharati Singh<br>
> <<a href="mailto:bharati0307@gmail.com">bharati0307@gmail.com</a> <mailto:<a href="mailto:bharati0307@gmail.com">bharati0307@gmail.com</a>>> wrote:<br>
><br>
> Hi Team,<br>
><br>
> I have LSF in my cluster ,I have installed gromacs-4.0.7 on<br>
> Sampige. It is working fine as a serial(on 1 processor) ,when<br>
> I submit the job for more than one processors in queue, it<br>
> gets terminated immediately.Can you suggest me something about<br>
> it, please<br>
><br>
> Thanks & Regards,<br>
><br>
> --<br>
> Bharati Singh<br>
> System Administrator<br>
> Centre for Computational Materials Science(CCMS)<br>
> Jawaharlal Nehru Centre for Advanced Scientific Research(JNCASR),<br>
> Bangalore - 560 064<br>
> India.<br>
> mob. : 08970898515<br>
> Phone : +91 80 2208 2944 + Ext. 26 & 28<br>
> Fax : +91 80 2208 2906<br>
> Email : <a href="mailto:bharati_singh@jncasr.ac.in">bharati_singh@jncasr.ac.in</a> <mailto:<a href="mailto:amit@jncasr.ac.in">amit@jncasr.ac.in</a>><br>
><br>
><br>
> <a href="http://www.jncasr.ac.in/ccms" target="_blank">http://www.jncasr.ac.in/ccms</a><br>
> <a href="http://www.jncasr.ac.in/" target="_blank">http://www.jncasr.ac.in/</a><br>
><br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <mailto:<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at<br>
> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before<br>
> posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>
> <mailto:<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br>
> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
><br>
><br>
><br>
><br>
> --<br>
> -------------------------------------------------------------------<br>
> Saikat Banerjee<br>
> Integrated Ph.D student<br>
> Prof B. Bagchi's group<br>
> Room no. 210<br>
> Solid State and Structural Chemistry Unit (SSCU)<br>
> Indian Institute of Science<br>
> Bangalore-560012<br>
><br>
> Ph: +91-80-22933305 (lab)<br>
> +91-80-23602338 (lab)<br>
> +91-9980228606 (mobile)<br>
><br>
> Alternate e-mail:<br>
> <a href="mailto:saikat@sscu.iisc.ernet.in">saikat@sscu.iisc.ernet.in</a> <mailto:<a href="mailto:saikat@sscu.iisc.ernet.in">saikat@sscu.iisc.ernet.in</a>><br>
> <a href="mailto:banskt@yahoo.co.in">banskt@yahoo.co.in</a> <mailto:<a href="mailto:banskt@yahoo.co.in">banskt@yahoo.co.in</a>><br>
> -------------------------------------------------------------------<br>
><br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <mailto:<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at<br>
> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>
> <mailto:<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br>
> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
><br>
><br>
><br>
><br>
> --<br>
> Bharati Singh<br>
> System Administrator<br>
> Centre for Computational Materials Science(CCMS)<br>
> Jawaharlal Nehru Centre for Advanced Scientific Research(JNCASR),<br>
> Bangalore - 560 064<br>
> India.<br>
> mob. : 08970898515<br>
> Phone : +91 80 2208 2944 + Ext. 26 & 28<br>
> Fax : +91 80 2208 2906<br>
> Email : <a href="mailto:bharati_singh@jncasr.ac.in">bharati_singh@jncasr.ac.in</a> <mailto:<a href="mailto:amit@jncasr.ac.in">amit@jncasr.ac.in</a>><br>
><br>
><br>
> <a href="http://www.jncasr.ac.in/ccms" target="_blank">http://www.jncasr.ac.in/ccms</a><br>
> <a href="http://www.jncasr.ac.in/" target="_blank">http://www.jncasr.ac.in/</a><br>
<br>
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------------------------------<br>
<br>
Message: 3<br>
Date: Tue, 3 May 2011 15:49:47 +0530<br>
From: Bharati Singh <<a href="mailto:bharati0307@gmail.com">bharati0307@gmail.com</a>><br>
Subject: Re: [gmx-users] running job parallel<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <BANLkTinW1Lu-oZqV=bYfcB32sBuyBo=<a href="mailto:r9g@mail.gmail.com">r9g@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Mentioned method is working in another user's home directory on same<br>
machine, then I dont think the problem with linking.<br>
<br>
<br>
<br>
On Tue, May 3, 2011 at 3:34 PM, Mark Abraham <<a href="mailto:Mark.Abromeaham@anu.edu.au">Mark.Abromeaham@anu.edu.au</a>>wrote:<br>
<br>
> On 3/05/2011 7:37 PM, Bharati Singh wrote:<br>
><br>
> Hi Team,<br>
><br>
> Thanks for your reply.<br>
><br>
> I had tried following method to install gromacs-4.0.7 -<br>
><br>
> $ module load intel_all/impi/default<br>
><br>
> $ ./configure --enable-mpi --with-fft=fftw2<br>
> LDFLAGS="-L/sfs1/lib/sfftw-2.1.5/lib/"<br>
> CPPFLAGS="-I/sfs1/lib/sfftw-2.1.5/include" LIBS="-lsfftw" F77=mpif77<br>
> --prefix=/sfs3/home/bharati/gromacs<br>
><br>
> $ make<br>
> $ make install<br>
><br>
> Following the command to submit the job in queue:<br>
><br>
> bsub -q normal4c -n 4 mpirun -srun /sfs3/home/bharati/gromacs/bin/mdrun<br>
> -pd -v -s Ag6A12_equil.tpr -o Ag6A12_equil.trr -c Ag6A12_equil.gro -e<br>
> Ag6A12_equil.edr -g Ag6A12_equil.log<br>
><br>
><br>
> When I submit the job for more than one processors in queue, it gets<br>
> terminated immediately without error. It is not creating any file etc..<br>
><br>
><br>
> That set of commands should create mdrun_mpi. Why are you not using it?<br>
><br>
> If this mdrun really is the one produced by the above configuration, the<br>
> symptoms suggest some kind of (dynamic) linking problem, but we have no way<br>
> to be more specific. It's not GROMACS-related.<br>
><br>
> Mark<br>
><br>
><br>
><br>
> Thanks & Regards,<br>
><br>
> On Tue, May 3, 2011 at 2:40 PM, Saikat Banerjee <<a href="mailto:banskt.saikat@gmail.com">banskt.saikat@gmail.com</a>>wrote:<br>
><br>
>> Hi,<br>
>><br>
>> Have you checked the error log? Please post the error log.<br>
>><br>
>> Have you configured GROMACS using --enable-mpi?<br>
>><br>
>> Thanks,<br>
>> Saikat<br>
>><br>
>> On Tue, May 3, 2011 at 2:35 PM, Bharati Singh <<a href="mailto:bharati0307@gmail.com">bharati0307@gmail.com</a>>wrote:<br>
>><br>
>>> Hi Team,<br>
>>><br>
>>> I have LSF in my cluster ,I have installed gromacs-4.0.7 on Sampige. It<br>
>>> is working fine as a serial(on 1 processor) ,when I submit the job for<br>
>>> more than one processors in queue, it gets terminated immediately.Can you<br>
>>> suggest me something about it, please<br>
>>><br>
>>> Thanks & Regards,<br>
>>><br>
>>> --<br>
>>> Bharati Singh<br>
>>> System Administrator<br>
>>> Centre for Computational Materials Science(CCMS)<br>
>>> Jawaharlal Nehru Centre for Advanced Scientific Research(JNCASR),<br>
>>> Bangalore - 560 064<br>
>>> India.<br>
>>> mob. : 08970898515<br>
>>> Phone : +91 80 2208 2944 + Ext. 26 & 28<br>
>>> Fax : +91 80 2208 2906<br>
>>> Email : <a href="mailto:bharati_singh@jncasr.ac.in">bharati_singh@jncasr.ac.in</a> <<a href="mailto:amit@jncasr.ac.in">amit@jncasr.ac.in</a>><br>
>>><br>
>>><br>
>>> <a href="http://www.jncasr.ac.in/ccms" target="_blank">http://www.jncasr.ac.in/ccms</a><br>
>>> <a href="http://www.jncasr.ac.in/" target="_blank">http://www.jncasr.ac.in/</a><br>
>>><br>
>>> --<br>
>>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
>>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
>>> Please search the archive at<br>
>>> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
>>> Please don't post (un)subscribe requests to the list. Use the<br>
>>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
>>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
>>><br>
>><br>
>><br>
>><br>
>> --<br>
>> -------------------------------------------------------------------<br>
>> Saikat Banerjee<br>
>> Integrated Ph.D student<br>
>> Prof B. Bagchi's group<br>
>> Room no. 210<br>
>> Solid State and Structural Chemistry Unit (SSCU)<br>
>> Indian Institute of Science<br>
>> Bangalore-560012<br>
>><br>
>> Ph: +91-80-22933305 (lab)<br>
>> +91-80-23602338 (lab)<br>
>> +91-9980228606 (mobile)<br>
>><br>
>> Alternate e-mail:<br>
>> <a href="mailto:saikat@sscu.iisc.ernet.in">saikat@sscu.iisc.ernet.in</a><br>
>> <a href="mailto:banskt@yahoo.co.in">banskt@yahoo.co.in</a><br>
>> -------------------------------------------------------------------<br>
>><br>
>> --<br>
>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
>> Please search the archive at<br>
>> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
>> Please don't post (un)subscribe requests to the list. Use the<br>
>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
>><br>
><br>
><br>
><br>
> --<br>
> Bharati Singh<br>
> System Administrator<br>
> Centre for Computational Materials Science(CCMS)<br>
> Jawaharlal Nehru Centre for Advanced Scientific Research(JNCASR),<br>
> Bangalore - 560 064<br>
> India.<br>
> mob. : 08970898515<br>
> Phone : +91 80 2208 2944 + Ext. 26 & 28<br>
> Fax : +91 80 2208 2906<br>
> Email : <a href="mailto:bharati_singh@jncasr.ac.in">bharati_singh@jncasr.ac.in</a> <<a href="mailto:amit@jncasr.ac.in">amit@jncasr.ac.in</a>><br>
><br>
><br>
> <a href="http://www.jncasr.ac.in/ccms" target="_blank">http://www.jncasr.ac.in/ccms</a><br>
> <a href="http://www.jncasr.ac.in/" target="_blank">http://www.jncasr.ac.in/</a><br>
><br>
><br>
><br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at<br>
> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
><br>
<br>
<br>
<br>
--<br>
Bharati Singh<br>
System Administrator<br>
Centre for Computational Materials Science(CCMS)<br>
Jawaharlal Nehru Centre for Advanced Scientific Research(JNCASR),<br>
Bangalore - 560 064<br>
India.<br>
mob. : 08970898515<br>
Phone : +91 80 2208 2944 + Ext. 26 & 28<br>
Fax : +91 80 2208 2906<br>
Email : <a href="mailto:bharati_singh@jncasr.ac.in">bharati_singh@jncasr.ac.in</a> <<a href="mailto:amit@jncasr.ac.in">amit@jncasr.ac.in</a>><br>
<br>
<br>
<a href="http://www.jncasr.ac.in/ccms" target="_blank">http://www.jncasr.ac.in/ccms</a><br>
<a href="http://www.jncasr.ac.in/" target="_blank">http://www.jncasr.ac.in/</a><br>
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End of gmx-users Digest, Vol 85, Issue 19<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br><i><font face="garamond, serif"><b><span style="font-size: large;">Geethu Issac</span></b></font></i><div><span style="border-collapse: collapse;"><div><b><i><span style="border-collapse: separate;"><br>
<font face="garamond, serif"><span style="font-size: large;">"A life spent making mistakes is not only more honorable, but more useful than a life spent doing nothing." <br>-George Bernard Shaw</span></font></span></i></b></div>
<div style="font-family: arial,sans-serif; font-size: 13px;"><br></div><font face="arial, sans-serif"><font color="#888888"></font></font></span><font color="#888888"></font><font color="#888888"></font></div><br>