[gmx-users] Re: gmx-users Digest, Vol 48, Issue 54
Mukesh K Srivastava
srimks11 at gmail.com
Fri Apr 18 08:50:23 CEST 2008
I had tried the same for single node as -np 1 in my local m/c.
BR
On Fri, Apr 18, 2008 at 6:33 AM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. GDB Debugging - GROMACS(v-3.3.3) Application with
> OpenMPI(v-1.2.5/v-1.2.6) (Mukesh K Srivastava)
> 2. Re: GDB Debugging - GROMACS(v-3.3.3) Application with
> OpenMPI(v-1.2.5/v-1.2.6) (David van der Spoel)
> 3. Re: epsilon in mdp (David van der Spoel)
> 4. Conformation search! (Anthony Cruz)
> 5. Re: query about .xpm file (David van der Spoel)
> 6. water flow in CNT (Hero)
> 7. water in channel by "Dowser" (Hero)
> 8. Re: dielectric constant (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 17 Apr 2008 23:06:50 +0530
> From: "Mukesh K Srivastava" <srimks11 at gmail.com>
> Subject: [gmx-users] GDB Debugging - GROMACS(v-3.3.3) Application with
> OpenMPI(v-1.2.5/v-1.2.6)
> To: gmx-developers at gromacs.org, gmx-users at gromacs.org
> Cc: gmx-announce at gromacs.org
> Message-ID:
> <3efa6bfc0804171036y26bce920vdb332fed3837f675 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi.
>
> Anyone had performed GDB debugging for Gromacs(v3.x - v3.3.3) application
> with FFTW(v3.1) using OpenMPI(v-1.2.5 or v-1.2.6). I had properly
> configured
> OpenMPI with debug option and also configured Gromacs alongwith FFTW
> succesfully. I can perform p2bdbx_mpi, editconf_mpi, genbox_mpi,
> grompp_mpi
> compilation and finally mdrun_mpi without any error or warning messages.
> But
> while executing mdrun_mpi w.r.t mprun, I get libmpi.so.0 not found.
>
> I had tried with LD_LIBRARY_PATH, forcefully mentioning PATH &
> LD_LIBRARY_PATH in etc/bashrc file and also tried with providing softlink
> to
> libmpi.so.0, but everytime I get same error message of "libmpi.so.0" not
> found.
>
> I had check ldd and it's dependency of executable mdrun_mpi, checked it's
> symbol table content, and finally all lib's configured for 64 bit with ELF
> format but still getting same error of libmpi.so.0 not found while
> performing GDB serial debugging with single node.
>
> Note: I had performed GDB debugging for small MPI program(hello world)
> using
> OpenMPI(v1.2.5/v1.2.6) wthout GROMACS association succesfully.
>
> Any clue plz?
>
> BR
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> ------------------------------
>
> Message: 2
> Date: Thu, 17 Apr 2008 20:51:52 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] GDB Debugging - GROMACS(v-3.3.3) Application
> with OpenMPI(v-1.2.5/v-1.2.6)
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <48079C48.5040901 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Mukesh K Srivastava wrote:
> > Hi.
> >
> > Anyone had performed GDB debugging for Gromacs(v3.x - v3.3.3)
> > application with FFTW(v3.1) using OpenMPI(v-1.2.5 or v-1.2.6). I had
> > properly configured OpenMPI with debug option and also configured
> > Gromacs alongwith FFTW succesfully. I can perform p2bdbx_mpi,
> > editconf_mpi, genbox_mpi, grompp_mpi compilation and finally mdrun_mpi
> > without any error or warning messages. But while executing mdrun_mpi
> > w.r.t mprun, I get libmpi.so.0 not found.
> >
> > I had tried with LD_LIBRARY_PATH, forcefully mentioning PATH &
> > LD_LIBRARY_PATH in etc/bashrc file and also tried with providing
> > softlink to libmpi.so.0, but everytime I get same error message of
> > "libmpi.so.0" not found.
> >
> > I had check ldd and it's dependency of executable mdrun_mpi, checked
> > it's symbol table content, and finally all lib's configured for 64 bit
> > with ELF format but still getting same error of libmpi.so.0 not found
> > while performing GDB serial debugging with single node.
> >
> > Note: I had performed GDB debugging for small MPI program(hello
> > world) using OpenMPI(v1.2.5/v1.2.6) wthout GROMACS association
> succesfully.
> >
> > Any clue plz?
> try
> ldd mdrun_mpi
> on the nodes. probably the mpi is not installed on the nodes.
>
> >
> > BR
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
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>
> --
> 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: 3
> Date: Thu, 17 Apr 2008 20:52:36 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] epsilon in mdp
> To: Vitaly Chaban <vvchaban at gmail.com>, Discussion list for
> GROMACS
> users <gmx-users at gromacs.org>
> Message-ID: <48079C74.20501 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Vitaly Chaban wrote:
> > Dear gromacs users,
> >
> > In the gromacs example mdp-file for water (/tutor/water) one can find
> > "
> > ; Dielectric constant (DC) for cut-off or DC of reaction field
> > epsilon-r = 1
> > "
> >
> > Does it mean that the simulation will be hold as if DC of H2O were
> > equal to the DC of vacuum? Does one need to correct it to the
> > corresponding experimental value for water to obtain a real system?
> >
>
>
> this is outdated. sorry about that. check onlin documentation.
>
> > Thanks,
> > Vitaly
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/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/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: 4
> Date: Thu, 17 Apr 2008 15:31:08 -0400
> From: Anthony Cruz <acb15885 at uprm.edu>
> Subject: [gmx-users] Conformation search!
> To: gmx-users at gromacs.org
> Message-ID: <200804171531.08356.acb15885 at uprm.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi User:
> We have a protein with two domains. This two domains were connected by two
> linkers of different length. We want to study the different conformation
> that
> the protein domains can adopt depending the length of the linkers without
> loosing the secondary structure feature present. I was thinking in use
> some
> position restrain in the backbone atoms of the domains and leave the
> linkers
> and all the side chains to move freely but this aproach will not let the
> system to change the conformation.
> I'm using GROMACS 3.2.1.
> With a dihedral constraint it will be posible to what I want to do?
> How can I do it?
> There is any other option to do this?
>
> Best Regards,
> Anthony
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 17 Apr 2008 22:26:49 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] query about .xpm file
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4807B289.8080408 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> Bert wrote:
> > Hi gmx-usrs,
> >
> > I use the program g_densmap to generate a xpm file, and then I convert
> > it to eps format with xpm2ps. It goes quite well except for the
> > illegible coordinates with the ticks. I wonder if I can set those
> > coodinates arbitrarily. I have tried to adjust the -bx, -by set and the
> > m2p input file, but I can not set the coordinates of the ticks with
> > regular integers. Thanks very much for suggestions.
>
> Apart from the options in the m2p file, you can also edit the xpm file,
> because the legends are in there.
> >
> > Bert
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>
>
> --
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 17 Apr 2008 16:16:18 -0700 (PDT)
> From: Hero <cjt0610 at yahoo.com>
> Subject: [gmx-users] water flow in CNT
> To: gmx-users at gromacs.org
> Message-ID: <438078.70334.qm at web32503.mail.mud.yahoo.com>
> Content-Type: text/plain; charset=us-ascii
>
> Dear All,
>
> I am simulating water transport in CNT under pressure.
>
> If I use periodic boundary conditions, how can I scale the
> water velocity? Otherwise the velocity will be going to heaven!
>
> Thank you very much!
>
> Hero
>
>
>
> ____________________________________________________________________________________
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>
> ------------------------------
>
> Message: 7
> Date: Thu, 17 Apr 2008 17:17:55 -0700 (PDT)
> From: Hero <cjt0610 at yahoo.com>
> Subject: [gmx-users] water in channel by "Dowser"
> To: gmx-users at gromacs.org
> Message-ID: <883544.65024.qm at web32506.mail.mud.yahoo.com>
> Content-Type: text/plain; charset=us-ascii
>
> Dear Gramacs,
>
> Anybody know where I can get "Dowser" for water in channel?
>
> Thanks a lot!
>
> [gmx-users] water in channel
> Eric Jakobsson jake at ncsa.uiuc.edu
> Mon Jan 19 22:50:02 CET 2004
> Previous message: [gmx-users] water in channel
> Next message: [gmx-users] water in channel
> Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
>
>
>
> Approach # 2) will not work for all channels. We published a paper in
> Biophys. J. a number of years ago in which we looked at water motion in
> the gramicidin channel with the protein immobile but the water at 300
> K. The water moved locally in the normal way, but had no motion along the
> channel at all. I am sure if we had started with the channel empty and
> the gramicidin frozen, it would never have filled, at least not in any
> reasonable time. On the other hand, for some channels if you don't
> immobilize them and you don't have contents in the lumen, the lumenal
> structure will become unstable. So approach # 1) (Dowser or some
> equivalent method) is the better way, based on our group's experience.
>
> Eric
>
> At 11:31 AM 1/19/2004 -0500, you wrote:
>
> >I can think of 2 options:
> >
> >1) There is a program called "Dowser" put out by J. Hermans' lab at
> >UNC-Chapel hill. It usually works very well.
> >
> >2) You can position restrain the channel and allow water and bilayer to
> >move freely during MD. It should not take long for water to enter the
> >channel ... that is, providing that it is actually supposed to do so.
> Water
> >is probably the fastest diffusing species in your system. You can take
> >advantage of this.
> >
> >David
> >
>
> >-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> >David Bostick Office: 262 Venable Hall
> >Dept. of Physics and Astronomy Phone: (919)962-0165
> >Program in Molecular and Cellular Biophysics
> >UNC-Chapel Hill
> >CB #3255 Phillips Hall dbostick at
> physics.unc.edu
> >Chapel Hill, NC 27599
> http://www.unc.edu/~dbostick <http://www.unc.edu/%7Edbostick>
>
> >=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
> >
> >On Mon, 19 Jan 2004, Itamar Kass wrote:
> >
> > > Hi all, I am currently working on a channel in a DMPC bilayer (and
> > water). After inserting the channel into the bilayer (using Graham's
> > modified mdrun) I am facing a new problem. I want to put water in the
> > channel and did not succeed in doing it. Using pr simulation I did not
> > succeed, then I tried to use genbox, but it puts water in the membrane
> also.
> > > Does someone have an idea or face it and has a solution?
> > > Thank you, Itamar.
> > >
> > > ********************************************
> > > Computers are like airconditioners... They don't work well with
> Windows
> > open.
> > > ********************************************
> > >
> > > ===========================================
> > > | Itamar Kass
> > > | The Alexander Silberman
> > > | Institute of Life Sciences
> > > | Department of Biological Chemistry
> > > | The Hebrew University, Givat-Ram
> > > | Jerusalem, 91904, Israel
> > > | Tel: +972-(0)2-6585146
> > > | Fax: +972-(0)2-6584329
> > > | Email: ikass at cc.huji.ac.il
> > > | Homepage:
> > http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html<http://www.ls.huji.ac.il/%7Emembranelab/itamar/itamar_homepage.html>
> > > ============================================
> >
> >_______________________________________________
> >gmx-users mailing list
> >gmx-users at gromacs.org
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> >www interface or send it to gmx-users-request at gromacs.org.
>
> ---------------------------------
> Eric Jakobsson, Ph.D.
> Professor, Department of Molecular and Integrative Physiology, and of
> Biochemistry
> Senior Research Scientist, National Center for Supercomputing Applications
> Professor, Beckman Institute for Advanced Science and Technology
> 4021 Beckman Institute, mc251
> University of Illinois, Urbana, IL 61801
> ph. 217-244-2896 fax 217-244-2909
> (Currently on leave to the National Institutes of Health in Bethesda,
> Maryland, to be Director of the NIGMS Center for Bioinformatics and
> Computational Biology and Chair of the NIH Biomedical Information Science
> and Technology Initiative Consortium, but maintaining my research lab at
> Illinois by periodic commuting. My usual schedule is four days a week at
> NIH and three days a week at Illinois.)
>
>
>
> ____________________________________________________________________________________
> Be a better friend, newshound, and
> know-it-all with Yahoo! Mobile. Try it now.
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>
> ------------------------------
>
> Message: 8
> Date: Fri, 18 Apr 2008 11:02:27 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] dielectric constant
> To: Gromacs Users <gmx-users at gromacs.org>
> Message-ID: <4807F323.1080604 at anu.edu.au>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> gadies at fh.huji.ac.il wrote:
> > Dear Mark,
>
> Please leave traffic on the list for all to learn from and so that the
> conversation gets archived.
>
> > Is there somewhere I can read about this?
>
> Not that I know of.
>
> > Do you have an example of a similar simulation that has been done?
>
> No. I was commenting based on my GROMACS experience, not my experience
> of your intended problem type.
>
> Mark
>
>
> ------------------------------
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
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>
> End of gmx-users Digest, Vol 48, Issue 54
> *****************************************
>
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