Hi Dr .Warren, <br><br>Yes I tried without pull code. Atleast I ran for 10ns and it works (i.e DPPC bilayer with a butane molecule in the water). I am not sure why it doesnt work with pull code. <br><br>Mohan<br><br><br><br>
<br><div><span class="gmail_quote">On 13/04/06, <b class="gmail_sendername"><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a></b> <<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org
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</a><br><br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of gmx-users digest..."<br><br><br>Today's Topics:<br><br> 1. RE: Using Pull code with Coarse grain model (Dallas B. Warren)
<br> 2. (error in MD run) (jahanshah ashkani)<br> 3. REMD (Dongsheng Zhang)<br> 4. Re: REMD (Mark Abraham)<br> 5. Re: REMD (Dongsheng Zhang)<br> 6. Re: REMD (David van der Spoel)<br> 7. Re: Using Pull code with Coarse grain model (David van der Spoel)
<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Thu, 13 Apr 2006 10:36:04 +1000<br>From: "Dallas B. Warren" <<a href="mailto:Dallas.Warren@vcp.monash.edu.au">
Dallas.Warren@vcp.monash.edu.au</a>><br>Subject: RE: [gmx-users] Using Pull code with Coarse grain model<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>>
<br>Message-ID:<br> <<a href="mailto:89907EA1DCFB7548A431C13A270F9DD5018D4468@prk-exch-01.vcp.local">89907EA1DCFB7548A431C13A270F9DD5018D4468@prk-exch-01.vcp.local</a>><br>Content-Type: text/plain; charset=us-ascii
<br><br>Mohan,<br><br>What happens if you run it without using the pull code? i.e. is it a MD<br>parameter problem or something to do with the pull code specifically.<br><br>Catch ya,<br><br>Dr. Dallas Warren<br>Lecturer<br>
Department of Pharmaceutical Biology and Pharmacology<br>Victorian College of Pharmacy, Monash University<br>381 Royal Parade, Parkville VIC 3010<br><a href="mailto:dallas.warren@vcp.monash.edu.au">dallas.warren@vcp.monash.edu.au
</a><br>+61 3 9903 9524<br>---------------------------------<br>When the only tool you own is a hammer, every problem begins to resemble<br>a nail.<br><br><br>------------------------------<br><br>Message: 2<br>Date: Wed, 12 Apr 2006 21:16:14 -0700 (PDT)
<br>From: jahanshah ashkani <<a href="mailto:ashkani_2003@yahoo.com">ashkani_2003@yahoo.com</a>><br>Subject: [gmx-users] (error in MD run)<br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Message-ID: <
<a href="mailto:20060413041614.30959.qmail@web50409.mail.yahoo.com">20060413041614.30959.qmail@web50409.mail.yahoo.com</a>><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>Hi,<br> I have a problem in md run:
<br> "Fatal error: realloc for nlist->jjnr (160825344 bytes, file ns.c, line 368, nlis t->jjnr=0x0x64960020): No such file or directory"<br> My .tpr and .top files are including:<br><br> [ molecules ]<br> ; Compound #mols
<br> Protein 1<br> SOL 686247<br> NA+ 131<br><br> And .mdp file is including:<br><br> title =<br> cpp = cpp<br> include =
<br> define = -DFLEXIBLE<br> integrator = steep<br> tinit = 0<br> dt = 0.001<br> nsteps = 400<br> Tcoupl = berendsen
<br> tc_grps = protein sol NA+<br> tau_t = 0.1 0.1 0.1<br> Ref_t = 300 300 300<br> emtol = 0.00001<br> emstep =
0.1<br> nstcgsteep = 1000<br><br> I would be glad if someone helps me in this case.<br> Thank you very much.<br><br> Best,<br> Jahanshah Ashkani<br><br><br><br><br>---------------------------------<br>New Yahoo! Messenger with Voice. Call regular phones from your PC and save big.
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</a><br><br>------------------------------<br><br>Message: 3<br>Date: Thu, 13 Apr 2006 01:06:52 -0400<br>From: Dongsheng Zhang <<a href="mailto:dong@pampas.chem.purdue.edu">dong@pampas.chem.purdue.edu</a>><br>Subject: [gmx-users] REMD
<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:1144904812.10367.15.camel@pampas.chem.purdue.edu">1144904812.10367.15.camel@pampas.chem.purdue.edu
</a>><br>Content-Type: text/plain<br><br>Dear gmx users:<br><br>I am trying to run REMD with two replicas (for testing). I used<br>grompp -f -c -p -o replica0 to get replica0.tpr<br>grompp -f -c -p -o replica1 to get replica1.tpr
<br><br>then used<br>mdrun_mpi -np 2 -multi -replex 500 -reseed -1 -s replica -deffnm replica<br>-v -N 2<br>to run it.<br><br>I got an error message "Segmentation fault" from my script output, but<br>no error message in both log files. When I tried to run individual tpr
<br>file, it worked fine.<br><br>Could someone can comment why I got "Segmentation fault"? Thank you for<br>your help!<br><br><br>Dongsheng<br><br><br><br><br>------------------------------<br><br>Message: 4<br>
Date: Thu, 13 Apr 2006 15:17:30 +1000 (EST)<br>From: "Mark Abraham" <<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>><br>Subject: Re: [gmx-users] REMD<br>To: "Discussion list for GROMACS users" <
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID:<br> <<a href="mailto:58846.150.203.7.225.1144905450.squirrel@sqmail.anu.edu.au">58846.150.203.7.225.1144905450.squirrel@sqmail.anu.edu.au
</a>><br>Content-Type: text/plain;charset=iso-8859-1<br><br>> Dear gmx users:<br>><br>> I am trying to run REMD with two replicas (for testing). I used<br>> grompp -f -c -p -o replica0 to get replica0.tpr<br>
> grompp -f -c -p -o replica1 to get replica1.tpr<br>><br>> then used<br>> mdrun_mpi -np 2 -multi -replex 500 -reseed -1 -s replica -deffnm replica<br>> -v -N 2<br>> to run it.<br><br>mdrun doesn't take '-N 2' but I'm not sure this is the problem. Otherwise,
<br>looks fine to me.<br><br>> I got an error message "Segmentation fault" from my script output, but<br>> no error message in both log files. When I tried to run individual tpr<br>> file, it worked fine.
<br>><br>> Could someone can comment why I got "Segmentation fault"? Thank you for<br>> your help!<br><br>Your MPI setup might require you use a command like "mpirun -N 2 mdrun_mpi<br>..." to make it work - the segfault might be a gromacs-MPI interaction
<br>problem. If you can run an MPI process from the command line you may get<br>more helpful feedback.<br><br>Mark<br><br><br><br>------------------------------<br><br>Message: 5<br>Date: Thu, 13 Apr 2006 02:42:20 -0400<br>
From: Dongsheng Zhang <<a href="mailto:dong@pampas.chem.purdue.edu">dong@pampas.chem.purdue.edu</a>><br>Subject: Re: [gmx-users] REMD<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:1144910541.16761.8.camel@pampas.chem.purdue.edu">1144910541.16761.8.camel@pampas.chem.purdue.edu</a>><br>Content-Type: text/plain<br><br>dear Mark,<br><br>
Thank you very much for your prompt reply. I try to use parallel<br>computing. It works fine.<br>for example: grompp -f -c -p -o replica0 -np 2 -sort -shuffle<br> to get replica0.tpr<br> then, mdrun_mpi -np 2 -s
replica0.tpr<br><br><br>The error message mentioned in the previous email looks very strange to<br>me. MPI works fine, and individual tpr runs fine. The error message<br>comes out before replica exchange. replica0 stops at step 500, replica1
<br>stops at step 400, even the output informatio can't be complted. The<br>last lines in replica1.log is<br><br> Step Time Lambda<br> 400 0.80000 0.00000<br><br> Rel. Constraint Deviation: Max between atoms RMS
<br><br><br>I hope these further information can help you to figure out what's the<br>problem.<br><br>Best Wishes!<br><br>Dongsheng<br><br><br>On Thu, 2006-04-13 at 15:17 +1000, Mark Abraham wrote:<br>> > Dear gmx users:
<br>> ><br>> > I am trying to run REMD with two replicas (for testing). I used<br>> > grompp -f -c -p -o replica0 to get replica0.tpr<br>> > grompp -f -c -p -o replica1 to get replica1.tpr<br>> >
<br>> > then used<br>> > mdrun_mpi -np 2 -multi -replex 500 -reseed -1 -s replica -deffnm replica<br>> > -v -N 2<br>> > to run it.<br>><br>> mdrun doesn't take '-N 2' but I'm not sure this is the problem. Otherwise,
<br>> looks fine to me.<br>><br>> > I got an error message "Segmentation fault" from my script output, but<br>> > no error message in both log files. When I tried to run individual tpr<br>> > file, it worked fine.
<br>> ><br>> > Could someone can comment why I got "Segmentation fault"? Thank you for<br>> > your help!<br>><br>> Your MPI setup might require you use a command like "mpirun -N 2 mdrun_mpi
<br>> ..." to make it work - the segfault might be a gromacs-MPI interaction<br>> problem. If you can run an MPI process from the command line you may get<br>> more helpful feedback.<br>><br>> Mark<br>
><br>> _______________________________________________<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
http://www.gromacs.org/mailman/listinfo/gmx-users</a><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/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br><br><br>------------------------------<br><br>Message: 6<br>Date: Thu, 13 Apr 2006 09:52:42 +0200
<br>From: David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>><br>Subject: Re: [gmx-users] REMD<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:443E034A.2020603@xray.bmc.uu.se">443E034A.2020603@xray.bmc.uu.se</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br>Dongsheng Zhang wrote:<br>> dear Mark,
<br>><br>> Thank you very much for your prompt reply. I try to use parallel<br>> computing. It works fine.<br>> for example: grompp -f -c -p -o replica0 -np 2 -sort -shuffle<br>> to get replica0.tpr
<br>> then, mdrun_mpi -np 2 -s replica0.tpr<br>><br><br>please give EXACT command line and do use mpirun<br><br><br>><br>> The error message mentioned in the previous email looks very strange to<br>
> me. MPI works fine, and individual tpr runs fine. The error message<br>> comes out before replica exchange. replica0 stops at step 500, replica1<br>> stops at step 400, even the output informatio can't be complted. The
<br>> last lines in replica1.log is<br>><br>> Step Time Lambda<br>> 400 0.80000 0.00000<br>><br>> Rel. Constraint Deviation: Max between atoms RMS
<br>><br>><br>> I hope these further information can help you to figure out what's the<br>> problem.<br>><br>> Best Wishes!<br>><br>> Dongsheng<br>><br>><br>> On Thu, 2006-04-13 at 15:17 +1000, Mark Abraham wrote:
<br>>>> Dear gmx users:<br>>>><br>>>> I am trying to run REMD with two replicas (for testing). I used<br>>>> grompp -f -c -p -o replica0 to get replica0.tpr<br>>>> grompp -f -c -p -o replica1 to get
replica1.tpr<br>>>><br>>>> then used<br>>>> mdrun_mpi -np 2 -multi -replex 500 -reseed -1 -s replica -deffnm replica<br>>>> -v -N 2<br>>>> to run it.<br>>> mdrun doesn't take '-N 2' but I'm not sure this is the problem. Otherwise,
<br>>> looks fine to me.<br>>><br>>>> I got an error message "Segmentation fault" from my script output, but<br>>>> no error message in both log files. When I tried to run individual tpr
<br>>>> file, it worked fine.<br>>>><br>>>> Could someone can comment why I got "Segmentation fault"? Thank you for<br>>>> your help!<br>>> Your MPI setup might require you use a command like "mpirun -N 2 mdrun_mpi
<br>>> ..." to make it work - the segfault might be a gromacs-MPI interaction<br>>> problem. If you can run an MPI process from the command line you may get<br>>> more helpful feedback.<br>>><br>
>> Mark<br>>><br>>> _______________________________________________<br>>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
http://www.gromacs.org/mailman/listinfo/gmx-users</a><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/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>> _______________________________________________<br>> gmx-users mailing list
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please don't post (un)subscribe requests to the list. Use the
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</a><br><br><br>--<br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.
<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org
</a> <a href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br><br><br>------------------------------<br><br>Message: 7<br>Date: Thu, 13 Apr 2006 09:53:29 +0200
<br>From: David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>><br>Subject: Re: [gmx-users] Using Pull code with Coarse grain model<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:443E0379.3020608@xray.bmc.uu.se">443E0379.3020608@xray.bmc.uu.se</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br>Mohan Boggara wrote:
<br>> Hi all,<br>><br>> I am trying to use the pull code for constrained force method in a<br>> coarse grain dppc bilayer model developed by Dr. S.J. Marrink. But I am<br>> getting error message Warning: pressure scaling > 1% . The problem
<br>> persist even after I changed the tau_p from 1.0 to 1.5.<br>> Has anyone had any success on similar runs.<br>><br>change it to 20 or 50.<br><br><br><br><br>> Mohan<br>><br>> --<br>> Mohan Boggara
<br>> Department of Chemical Engineering<br>> University of Houston<br>> S222 Engineering Bldg 1<br>> Houston, Texas-77204, USA<br>> Mobile: 1-713-259-2166<br>> Office: 1-713-743-4314<br>> <a href="http://polymer.chee.uh.edu/">
http://polymer.chee.uh.edu/</a><br>><br>> All human actions have one or more of these seven causes: chance,<br>> nature, compulsion, habit, reason, passion, and desire.-- Aristotle<br>><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://www.gromacs.org/mailman/listinfo/gmx-users">
http://www.gromacs.org/mailman/listinfo/gmx-users</a><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/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br><br><br>--<br>David.<br>________________________________________________________________________
<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755
<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
<br><br><br>------------------------------<br><br>_______________________________________________<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
http://www.gromacs.org/mailman/listinfo/gmx-users</a><br><br><br>End of gmx-users Digest, Vol 24, Issue 44<br>*****************************************<br></blockquote></div><br><br clear="all"><br>-- <br>Mohan Boggara<br>
Department of Chemical Engineering<br>University of Houston<br>S222 Engineering Bldg 1<br>Houston, Texas-77204, USA<br>Mobile: 1-713-259-2166<br>Office: 1-713-743-4314 <br><a href="http://polymer.chee.uh.edu/">http://polymer.chee.uh.edu/
</a><br><br>All human actions have one or more of these seven causes: chance, nature, compulsion, habit, reason, passion, and desire.-- Aristotle