[gmx-users] Re: gmx-users Digest, Vol 48, Issue 9
Justin A. Lemkul
jalemkul at vt.edu
Fri Apr 4 19:15:19 CEST 2008
You are going to want to do some thorough reading through tutorial materials to
start. May I suggest the following links:
http://wiki.gromacs.org/index.php/Beginners
http://wiki.gromacs.org/index.php/Category:Tutorials
-Justin
Quoting Collins Nganou <nganoucollins at gmail.com>:
> Dear all greeting
> I am a new user in gromacs .
> To begin, I need to know how to generate date for simple water
> molecule and observe
> vibrational modes.
> I use this command as well as read in the manual: pdb2gmx -f prot.pdb
> -o prot.gro -p prot.top
> but when I choose
>
> ff 43a1
> Opening library file /usr/share/gromacs/top/ffG43a1.rtp
> Opening library file /usr/share/gromacs/top/aminoacids.dat
> Reading prot.pdb...
>
> I have this error:
>
> Program pdb2gmx, VERSION 3.3.1
> Source code file: futil.c, line: 340
>
> File input/output error:
> prot.pdb
>
>
>
> On Fri, Apr 4, 2008 at 12:00 PM, <gmx-users-request at gromacs.org> wrote:
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> >
> > Today's Topics:
> >
> > 1. RE: difference between pbc = full and pbc =xy (Berk Hess)
> > 2. Re: genion problem: is replacing 84 water molecules instead
> > of 200 (David van der Spoel)
> > 3. Re: Test-set problem with Gromacs 3.3.3 (David van der Spoel)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Fri, 4 Apr 2008 03:50:40 +0200
> > From: Berk Hess <gmx3 at hotmail.com>
> > Subject: RE: [gmx-users] difference between pbc = full and pbc =xy
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <BLU134-W5137A2364ABCCE8FA81B2A8EF60 at phx.gbl>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Hi,
> >
> > All options are described in share/html/online/mdp_opt.html
> > pbc=xy is what you would (probably) guess pbc in x and y only.
> > pbc=full is replaced by periodic_molecules, such that it can also
> > be used with pbc=xy.
> >
> > Berk.
> >
> >
> > > From: zhoubo81 at gmail.com
> > > To: gmx-users at gromacs.org
> > > Date: Thu, 3 Apr 2008 11:55:22 +0800
> > > Subject: [gmx-users] difference between pbc = full and pbc =xy
> > >
> > > Dear all,
> > >
> > > I want to simulate an infinite inorganic surface in gmx 3.3.3 recently.
> As I
> > > know, pbc = full is required for the bonded interaction on the edges.
> When I
> > > check the newly CVS version, a new set named "pbc = xy" is implemented.
> I
> > > wonder if there is something different between the two sets. Thanks in
> > > advance.
> > >
> > >
> > >
> > > _______________________________________________
> > > gmx-users mailing list gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
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> posting!
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> >
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> > ------------------------------
> >
> > Message: 2
> > Date: Fri, 04 Apr 2008 08:08:44 +0200
> > From: David van der Spoel <spoel at xray.bmc.uu.se>
> > Subject: Re: [gmx-users] genion problem: is replacing 84 water
> > molecules instead of 200
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <47F5C5EC.8050208 at xray.bmc.uu.se>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > Subhrangshu Supakar wrote:
> > > Hi All !!
> > > I have defined my own system which contains 200 water molecules, which I
> > > can see in the .gro file. Then I created the .tpr file for 200 steps to
> > > steep. In the confout file I can again see the 200 water molecules. But
> > > When I am trying to replace the 200 water molecules with 200 Na+
> > > GROMACS is complaining:
> >
> > genion -h is your friend.
> >
> > check the -rmin option.
> > >
> > > Replacing solvent molecule 144 (atom 4632) with Na
> > > Replacing solvent molecule 193 (atom 4779) with Na
> > > Replacing solvent molecule 49 (atom 4347) with Na
> > > Replacing solvent molecule 84 (atom 4452) with Na
> > >
> > > -------------------------------------------------------
> > > Program genion, VERSION 3.3.2
> > > Source code file: gmx_genion.c, line: 84
> > >
> > > Fatal error:
> > > No more replaceable solvent!
> > > -------------------------------------------------------
> > > It is replacing 84 water molecules only (I used genion for this)
> > >
> > > Can any body help me?
> > >
> > > Thanx in advance.
> > >
> > > Subhrangshu Supakar
> > >
> > >
> > > ------------------------------------------------------------------------
> > >
> > > _______________________________________________
> > > 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: 3
> > Date: Fri, 04 Apr 2008 08:10:33 +0200
> > From: David van der Spoel <spoel at xray.bmc.uu.se>
> > Subject: Re: [gmx-users] Test-set problem with Gromacs 3.3.3
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <47F5C659.8080904 at xray.bmc.uu.se>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > janne.hirvi at joensuu.fi wrote:
> > > Dear gmx-users,
> > >
> > > I just updated my operating system to Centos 5.1 and Gromacs to version
> > > 3.3.3 and faced some problems with test-set (gmxtest-3.3.2.tgz). I can
> > > pass all the double precision tests (./gmxtest.pl -double all), but
> > > number of single precision tests are failed (./gmxtest.pl all). I looked
> > > at the files for these tests, and noticed that the corresponding tests
> > > include Coulombic and LJ 1-4 interactions, for which the calculated
> > > energies are all zero, whereas the reference energies are non-zero with
> > > values even 1000-2000 kJ/mol. Does anyone know reason for such
> differences?
> >
> > This actually points to possible compilation problems, and hence shows
> > the value of the test set. Please check every step in the compilation
> > process, and also which executable you are running (which mdrun) and
> > which libraries (ldd `which mdrun`).
> >
> >
> > >
> > > Thanks for your help,
> > >
> > > Janne
> > >
> > >
> ------------------------------------------------------------------------------
> > >
> > > Janne Hirvi, MSc(Physical Chemistry), Researcher
> > > University of Joensuu, Department of Chemistry, P.O.Box 111 80101
> > > Joensuu, FI
> > > Tel: +358 13 2514544 & +358 50 3474223
> > > E-mail: janne.hirvi at joensuu.fi & hirvi at cc.joensuu.fi
> > >
> ------------------------------------------------------------------------------
> > >
> > > _______________________________________________
> > > 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!
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> > > 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
> > Please search the archive at http://www.gromacs.org/search before posting!
> >
> > End of gmx-users Digest, Vol 48, Issue 9
> > ****************************************
> >
> _______________________________________________
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>
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
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