[gmx-users] Re: gmx-users Digest, Vol 48, Issue 9
Collins Nganou
nganoucollins at gmail.com
Fri Apr 4 18:44:06 CEST 2008
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.
> >
> >
> >
> > _______________________________________________
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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
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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: 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
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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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
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> End of gmx-users Digest, Vol 48, Issue 9
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