[gmx-users] Re: Using Pull code with Coarse grain model
Mohan Boggara
mohanbabu.boggara at gmail.com
Fri Apr 14 00:08:24 CEST 2006
Hi Dr .Warren,
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.
Mohan
On 13/04/06, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org>
wrote:
>
> Send gmx-users mailing list submissions to
> gmx-users at gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://www.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
> gmx-users-request at gromacs.org
>
> You can reach the person managing the list at
> gmx-users-owner at 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. RE: Using Pull code with Coarse grain model (Dallas B. Warren)
> 2. (error in MD run) (jahanshah ashkani)
> 3. REMD (Dongsheng Zhang)
> 4. Re: REMD (Mark Abraham)
> 5. Re: REMD (Dongsheng Zhang)
> 6. Re: REMD (David van der Spoel)
> 7. Re: Using Pull code with Coarse grain model (David van der Spoel)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 13 Apr 2006 10:36:04 +1000
> From: "Dallas B. Warren" <Dallas.Warren at vcp.monash.edu.au>
> Subject: RE: [gmx-users] Using Pull code with Coarse grain model
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <89907EA1DCFB7548A431C13A270F9DD5018D4468 at prk-exch-01.vcp.local>
> Content-Type: text/plain; charset=us-ascii
>
> Mohan,
>
> What happens if you run it without using the pull code? i.e. is it a MD
> parameter problem or something to do with the pull code specifically.
>
> Catch ya,
>
> Dr. Dallas Warren
> Lecturer
> Department of Pharmaceutical Biology and Pharmacology
> Victorian College of Pharmacy, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at vcp.monash.edu.au
> +61 3 9903 9524
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble
> a nail.
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 12 Apr 2006 21:16:14 -0700 (PDT)
> From: jahanshah ashkani <ashkani_2003 at yahoo.com>
> Subject: [gmx-users] (error in MD run)
> To: gmx-users at gromacs.org
> Message-ID: <20060413041614.30959.qmail at web50409.mail.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
> I have a problem in md run:
> "Fatal error: realloc for nlist->jjnr (160825344 bytes, file ns.c, line
> 368, nlis t->jjnr=0x0x64960020): No such file or directory"
> My .tpr and .top files are including:
>
> [ molecules ]
> ; Compound #mols
> Protein 1
> SOL 686247
> NA+ 131
>
> And .mdp file is including:
>
> title =
> cpp = cpp
> include =
> define = -DFLEXIBLE
> integrator = steep
> tinit = 0
> dt = 0.001
> nsteps = 400
> Tcoupl = berendsen
> tc_grps = protein sol NA+
> tau_t = 0.1 0.1 0.1
> Ref_t = 300 300 300
> emtol = 0.00001
> emstep = 0.1
> nstcgsteep = 1000
>
> I would be glad if someone helps me in this case.
> Thank you very much.
>
> Best,
> Jahanshah Ashkani
>
>
>
>
> ---------------------------------
> New Yahoo! Messenger with Voice. Call regular phones from your PC and save
> big.
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://www.gromacs.org/pipermail/gmx-users/attachments/20060412/b95f142f/attachment-0001.html
>
> ------------------------------
>
> Message: 3
> Date: Thu, 13 Apr 2006 01:06:52 -0400
> From: Dongsheng Zhang <dong at pampas.chem.purdue.edu>
> Subject: [gmx-users] REMD
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1144904812.10367.15.camel at pampas.chem.purdue.edu>
> Content-Type: text/plain
>
> Dear gmx users:
>
> I am trying to run REMD with two replicas (for testing). I used
> grompp -f -c -p -o replica0 to get replica0.tpr
> grompp -f -c -p -o replica1 to get replica1.tpr
>
> then used
> mdrun_mpi -np 2 -multi -replex 500 -reseed -1 -s replica -deffnm replica
> -v -N 2
> to run it.
>
> I got an error message "Segmentation fault" from my script output, but
> no error message in both log files. When I tried to run individual tpr
> file, it worked fine.
>
> Could someone can comment why I got "Segmentation fault"? Thank you for
> your help!
>
>
> Dongsheng
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 13 Apr 2006 15:17:30 +1000 (EST)
> From: "Mark Abraham" <mark.abraham at anu.edu.au>
> Subject: Re: [gmx-users] REMD
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID:
> <58846.150.203.7.225.1144905450.squirrel at sqmail.anu.edu.au>
> Content-Type: text/plain;charset=iso-8859-1
>
> > Dear gmx users:
> >
> > I am trying to run REMD with two replicas (for testing). I used
> > grompp -f -c -p -o replica0 to get replica0.tpr
> > grompp -f -c -p -o replica1 to get replica1.tpr
> >
> > then used
> > mdrun_mpi -np 2 -multi -replex 500 -reseed -1 -s replica -deffnm replica
> > -v -N 2
> > to run it.
>
> mdrun doesn't take '-N 2' but I'm not sure this is the problem. Otherwise,
> looks fine to me.
>
> > I got an error message "Segmentation fault" from my script output, but
> > no error message in both log files. When I tried to run individual tpr
> > file, it worked fine.
> >
> > Could someone can comment why I got "Segmentation fault"? Thank you for
> > your help!
>
> Your MPI setup might require you use a command like "mpirun -N 2 mdrun_mpi
> ..." to make it work - the segfault might be a gromacs-MPI interaction
> problem. If you can run an MPI process from the command line you may get
> more helpful feedback.
>
> Mark
>
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 13 Apr 2006 02:42:20 -0400
> From: Dongsheng Zhang <dong at pampas.chem.purdue.edu>
> Subject: Re: [gmx-users] REMD
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1144910541.16761.8.camel at pampas.chem.purdue.edu>
> Content-Type: text/plain
>
> dear Mark,
>
> Thank you very much for your prompt reply. I try to use parallel
> computing. It works fine.
> for example: grompp -f -c -p -o replica0 -np 2 -sort -shuffle
> to get replica0.tpr
> then, mdrun_mpi -np 2 -s replica0.tpr
>
>
> The error message mentioned in the previous email looks very strange to
> me. MPI works fine, and individual tpr runs fine. The error message
> comes out before replica exchange. replica0 stops at step 500, replica1
> stops at step 400, even the output informatio can't be complted. The
> last lines in replica1.log is
>
> Step Time Lambda
> 400 0.80000 0.00000
>
> Rel. Constraint Deviation: Max between atoms RMS
>
>
> I hope these further information can help you to figure out what's the
> problem.
>
> Best Wishes!
>
> Dongsheng
>
>
> On Thu, 2006-04-13 at 15:17 +1000, Mark Abraham wrote:
> > > Dear gmx users:
> > >
> > > I am trying to run REMD with two replicas (for testing). I used
> > > grompp -f -c -p -o replica0 to get replica0.tpr
> > > grompp -f -c -p -o replica1 to get replica1.tpr
> > >
> > > then used
> > > mdrun_mpi -np 2 -multi -replex 500 -reseed -1 -s replica -deffnm
> replica
> > > -v -N 2
> > > to run it.
> >
> > mdrun doesn't take '-N 2' but I'm not sure this is the problem.
> Otherwise,
> > looks fine to me.
> >
> > > I got an error message "Segmentation fault" from my script output, but
> > > no error message in both log files. When I tried to run individual tpr
> > > file, it worked fine.
> > >
> > > Could someone can comment why I got "Segmentation fault"? Thank you
> for
> > > your help!
> >
> > Your MPI setup might require you use a command like "mpirun -N 2
> mdrun_mpi
> > ..." to make it work - the segfault might be a gromacs-MPI interaction
> > problem. If you can run an MPI process from the command line you may get
> > more helpful feedback.
> >
> > Mark
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > 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/mailing_lists/users.php
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 13 Apr 2006 09:52:42 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] REMD
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <443E034A.2020603 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dongsheng Zhang wrote:
> > dear Mark,
> >
> > Thank you very much for your prompt reply. I try to use parallel
> > computing. It works fine.
> > for example: grompp -f -c -p -o replica0 -np 2 -sort -shuffle
> > to get replica0.tpr
> > then, mdrun_mpi -np 2 -s replica0.tpr
> >
>
> please give EXACT command line and do use mpirun
>
>
> >
> > The error message mentioned in the previous email looks very strange to
> > me. MPI works fine, and individual tpr runs fine. The error message
> > comes out before replica exchange. replica0 stops at step 500, replica1
> > stops at step 400, even the output informatio can't be complted. The
> > last lines in replica1.log is
> >
> > Step Time Lambda
> > 400 0.80000 0.00000
> >
> > Rel. Constraint Deviation: Max between atoms RMS
> >
> >
> > I hope these further information can help you to figure out what's the
> > problem.
> >
> > Best Wishes!
> >
> > Dongsheng
> >
> >
> > On Thu, 2006-04-13 at 15:17 +1000, Mark Abraham wrote:
> >>> Dear gmx users:
> >>>
> >>> I am trying to run REMD with two replicas (for testing). I used
> >>> grompp -f -c -p -o replica0 to get replica0.tpr
> >>> grompp -f -c -p -o replica1 to get replica1.tpr
> >>>
> >>> then used
> >>> mdrun_mpi -np 2 -multi -replex 500 -reseed -1 -s replica -deffnm
> replica
> >>> -v -N 2
> >>> to run it.
> >> mdrun doesn't take '-N 2' but I'm not sure this is the problem.
> Otherwise,
> >> looks fine to me.
> >>
> >>> I got an error message "Segmentation fault" from my script output, but
> >>> no error message in both log files. When I tried to run individual tpr
> >>> file, it worked fine.
> >>>
> >>> Could someone can comment why I got "Segmentation fault"? Thank you
> for
> >>> your help!
> >> Your MPI setup might require you use a command like "mpirun -N 2
> mdrun_mpi
> >> ..." to make it work - the segfault might be a gromacs-MPI interaction
> >> problem. If you can run an MPI process from the command line you may
> get
> >> more helpful feedback.
> >>
> >> Mark
> >>
> >> _______________________________________________
> >> gmx-users mailing list gmx-users at gromacs.org
> >> http://www.gromacs.org/mailman/listinfo/gmx-users
> >> 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/mailing_lists/users.php
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > 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/mailing_lists/users.php
>
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
> ------------------------------
>
> Message: 7
> Date: Thu, 13 Apr 2006 09:53:29 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Using Pull code with Coarse grain model
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <443E0379.3020608 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Mohan Boggara wrote:
> > Hi all,
> >
> > I am trying to use the pull code for constrained force method in a
> > coarse grain dppc bilayer model developed by Dr. S.J. Marrink. But I am
> > getting error message Warning: pressure scaling > 1% . The problem
> > persist even after I changed the tau_p from 1.0 to 1.5.
> > Has anyone had any success on similar runs.
> >
> change it to 20 or 50.
>
>
>
>
> > Mohan
> >
> > --
> > Mohan Boggara
> > Department of Chemical Engineering
> > University of Houston
> > S222 Engineering Bldg 1
> > Houston, Texas-77204, USA
> > Mobile: 1-713-259-2166
> > Office: 1-713-743-4314
> > http://polymer.chee.uh.edu/
> >
> > All human actions have one or more of these seven causes: chance,
> > nature, compulsion, habit, reason, passion, and desire.-- Aristotle
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > 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/mailing_lists/users.php
>
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
> ------------------------------
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
>
>
> End of gmx-users Digest, Vol 24, Issue 44
> *****************************************
>
--
Mohan Boggara
Department of Chemical Engineering
University of Houston
S222 Engineering Bldg 1
Houston, Texas-77204, USA
Mobile: 1-713-259-2166
Office: 1-713-743-4314
http://polymer.chee.uh.edu/
All human actions have one or more of these seven causes: chance, nature,
compulsion, habit, reason, passion, and desire.-- Aristotle
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060413/7f49af02/attachment.html>
More information about the gromacs.org_gmx-users
mailing list