[gmx-users] Grompp error (no default RB dihedral)
David
spoel at xray.bmc.uu.se
Sat Jun 11 09:42:22 CEST 2005
On Fri, 2005-06-10 at 17:06 -0500, Lakhani, Ahmed Ashiqali wrote:
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> In Opls-aa force field with Aib, using Grompp we also got warning on
> missing torsion angles. We looked up in ffoplsboni.itp, we couldn't find
> C-Ca-C-H entry. But Instead we found C-C-C-H. Is this okay to use or is
> there any other way.
Check torsion for Valine instead.
>
>
>
>
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> > Today's Topics:
> >
> > 1. Re: Question regarding installing fftw (David)
> > 2. Re: Question regarding installing fftw (Kai Zhuang)
> > 3. Re: gigabit scaling, DPPC benchmark (Marcos Villarreal)
> > 4. Re: Benchmarks (Nathan Moore)
> > 5. Re: Benchmarks (David)
> > 6. Re: gigabit scaling, DPPC benchmark (David)
> > 7. Re: Benchmarks (Nathan Moore)
> > 8. Re: Benchmarks (David)
> > 9. [Fwd: Grompp error (no default RB dihedral)] (David)
> > 10. Re: cell output (T.A.Wassenaar)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Tue, 07 Jun 2005 21:01:42 +0200
> > From: David <spoel at xray.bmc.uu.se>
> > Subject: Re: [gmx-users] Question regarding installing fftw
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <1118170902.23988.2.camel at localhost.localdomain>
> > Content-Type: text/plain
> >
> > On Tue, 2005-06-07 at 13:15 -0500, Michael Homa wrote:
> >> Hi:
> >>
> >> I apologize if this is an incredibly stupid question. I am
> >> installing Gromacs on our academic computing cluster. According to the
> >> "Prerequisites" page on the web:
> >>
> >> YOU NEED FFTW VERSION 2.1.5
> >>
> >> It's very specific about which version, 2.1.5. But, then in the next few
> >> paragraphs, there are four links to rpm files not for version
> >> 2.1.5 but for version 2.1.3.2:
> >>
> >> fftw-2.1.3-2.i386.rpm
> >> fftw-devel-2.1.3-2.i386.rpm
> >> fftw lammpi-2.1.3-2.i386.rpm
> >> fftw-lammpi-devel-2.1.3-2.i386.rpm
> >>
> >> Can I use the the 2.1.3-2 version instead of the 2.1.5? Thanks.
> >>
> > yes, but you do need single precision (lib*sfft* libraries).
> > try it.
> >
> >
> >> Michael Homa
> >> Operating Systems Support and Database Group
> >> Academic Computing and Communication Center
> >> University of Illinois at Chicago
> >> email: mhoma at uic.edu
> >>
> >> _______________________________________________
> >> 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://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Tue, 7 Jun 2005 15:01:16 -0400
> > From: Kai Zhuang <kai.zhuang at gmail.com>
> > Subject: Re: [gmx-users] Question regarding installing fftw
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <66c8725f050607120129055778 at mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > http://www.fftw.org/download.html
> >
> > searched it straight from google. 2.1.5 is on the page.
> >
> > don't use 2.3 cuz it doesn't have the support gromacs needs (i made
> > this mistake)
> >
> > gromacs has a good installation guide, follow it.
> >
> >
> >
> > On 6/7/05, Nathan Moore <nmoore at physics.umn.edu> wrote:
> >> I've gotten gromacs to run with fftw 2.1.5. I'm guessing its a typo
> >>
> >> nt moore
> >>
> >> > Hi:
> >> >
> >> > I apologize if this is an incredibly stupid question. I am
> >> > installing Gromacs on our academic computing cluster. According to the
> >> > "Prerequisites" page on the web:
> >> >
> >> > YOU NEED FFTW VERSION 2.1.5
> >> >
> >> > It's very specific about which version, 2.1.5. But, then in the next
> >> few
> >> > paragraphs, there are four links to rpm files not for version
> >> > 2.1.5 but for version 2.1.3.2:
> >> >
> >> > fftw-2.1.3-2.i386.rpm
> >> > fftw-devel-2.1.3-2.i386.rpm
> >> > fftw lammpi-2.1.3-2.i386.rpm
> >> > fftw-lammpi-devel-2.1.3-2.i386.rpm
> >> >
> >> > Can I use the the 2.1.3-2 version instead of the 2.1.5? Thanks.
> >> >
> >> > Michael Homa
> >> > Operating Systems Support and Database Group
> >> > Academic Computing and Communication Center
> >> > University of Illinois at Chicago
> >> > email: mhoma at uic.edu
> >> >
> >> > _______________________________________________
> >> > 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.
> >> >
> >>
> >> _______________________________________________
> >> 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
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> >>
> >
> >
> > --
> > Kai Zhuang
> > BioMedical Engineering @ University of Toronto
> > kai dot zhuang at gmail dot com
> > kai.zhuang at gmail.com
> > 6478314789
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Tue, 7 Jun 2005 16:20:20 -0300
> > From: Marcos Villarreal <arloa at mail.fcq.unc.edu.ar>
> > Subject: Re: [gmx-users] gigabit scaling, DPPC benchmark
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <200506071620.20982.arloa at mail.fcq.unc.edu.ar>
> > Content-Type: text/plain; charset="utf-8"
> >
> > On Tuesday 07 June 2005 16:04, David wrote:
> >>
> >> then it could still be hardware: switch, network card. Not all switches
> >> are equal. Maybe you can try other performance tests, if I'm not
> >> mistaken LAM comes with a set of tests.
> >>
> >
> > Can you please tell which switch and network card were used on the
> > computer of
> > the benchmark?
> >
> > Thanks,
> > Marcos Villarreal.
> >
> >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Tue, 7 Jun 2005 16:03:17 -0500 (CDT)
> > From: "Nathan Moore" <nmoore at physics.umn.edu>
> > Subject: Re: [gmx-users] Benchmarks
> > To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> > Message-ID:
> > <5671.129.42.161.36.1118178197.squirrel at mail.physics.umn.edu>
> > Content-Type: text/plain;charset=iso-8859-1
> >
> > Are the parallel benchmarks also expressed in terms of ps/day?
> >
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Tue, 07 Jun 2005 23:15:47 +0200
> > From: David <spoel at xray.bmc.uu.se>
> > Subject: Re: [gmx-users] Benchmarks
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <1118178947.4788.0.camel at localhost.localdomain>
> > Content-Type: text/plain
> >
> > On Tue, 2005-06-07 at 16:03 -0500, Nathan Moore wrote:
> >> Are the parallel benchmarks also expressed in terms of ps/day?
> > Yes.
> >
> >
> >> _______________________________________________
> >> 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.
> > --
> > 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://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> >
> >
> > ------------------------------
> >
> > Message: 6
> > Date: Tue, 07 Jun 2005 23:17:25 +0200
> > From: David <spoel at xray.bmc.uu.se>
> > Subject: Re: [gmx-users] gigabit scaling, DPPC benchmark
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <1118179045.4788.3.camel at localhost.localdomain>
> > Content-Type: text/plain
> >
> > On Tue, 2005-06-07 at 16:20 -0300, Marcos Villarreal wrote:
> >> On Tuesday 07 June 2005 16:04, David wrote:
> >> >
> >> > then it could still be hardware: switch, network card. Not all
> >> switches
> >> > are equal. Maybe you can try other performance tests, if I'm not
> >> > mistaken LAM comes with a set of tests.
> >> >
> >>
> >> Can you please tell which switch and network card were used on the
> >> computer of
> >> the benchmark?
> >
> > Erik L. did these tests if I'm not mistaken on a Dell cluster at
> > Stanford. See this link:
> >
> > http://www1.us.dell.com/content/topics/global.aspx/corp/pressoffice/en/2003/2003_09_08_pla_000?c=us&l=en&s=corp
> >>
> >> Thanks,
> >> Marcos Villarreal.
> >>
> >> _______________________________________________
> >> 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.
> > --
> > 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://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> >
> >
> > ------------------------------
> >
> > Message: 7
> > Date: Tue, 7 Jun 2005 16:21:17 -0500 (CDT)
> > From: "Nathan Moore" <nmoore at physics.umn.edu>
> > Subject: Re: [gmx-users] Benchmarks
> > To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> > Message-ID:
> > <32133.129.42.161.36.1118179277.squirrel at mail.physics.umn.edu>
> > Content-Type: text/plain;charset=iso-8859-1
> >
> > Are the benchmarks for specifically float-precision code? If so, are
> > similar figures available for double precision?
> >
> >
> > ------------------------------
> >
> > Message: 8
> > Date: Tue, 07 Jun 2005 23:34:11 +0200
> > From: David <spoel at xray.bmc.uu.se>
> > Subject: Re: [gmx-users] Benchmarks
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <1118180051.4788.7.camel at localhost.localdomain>
> > Content-Type: text/plain
> >
> > On Tue, 2005-06-07 at 16:21 -0500, Nathan Moore wrote:
> >> Are the benchmarks for specifically float-precision code? If so, are
> >> similar figures available for double precision?
> > They will soon be, for P4/Opteron it is a factor of two slower, for
> > Itanium the difference is less, for G5 the difference is more.
> >
> >> _______________________________________________
> >> 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.
> > --
> > 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://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> >
> >
> > ------------------------------
> >
> > Message: 9
> > Date: Wed, 08 Jun 2005 07:26:31 +0200
> > From: David <spoel at xray.bmc.uu.se>
> > Subject: [gmx-users] [Fwd: Grompp error (no default RB dihedral)]
> > To: gmx-users at gromacs.org
> > Message-ID: <1118208391.4789.0.camel at localhost.localdomain>
> > Content-Type: text/plain
> >
> > -------- Forwarded Message --------
> > From: Xiaoming Zhang <xzhang at artsci.wustl.edu>
> > Reply-To: xzhang at artsci.wustl.edu
> > To: David van der Spoel <spoel at xray.bmc.uu.se>
> > Subject: Grompp error (no default RB dihedral)
> > Date: Tue, 7 Jun 2005 17:41:33 -0500 (CDT)
> > Dear Dr. Spoel,
> >
> > I am a graduate student at Washington University in St. louis. Currently
> > I am
> > working on the MD simulation in oplsaa ff using GROMACS. My peptide has
> > an "AIB" residue. GROMPP complained that the six dihedrals (c-c-c-H) in
> > dimethyl group of AIB are not default RB type. I was wondering whether it
> > is
> > ok to ignore that warning and how to add parameters for those dihedrals if
> > I
> > want to fix the problem.
> >
> > Thank you very much,
> >
> > Xiaoming Zhang
> > --
> > 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://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> >
> >
> > ------------------------------
> >
> > Message: 10
> > Date: Wed, 08 Jun 2005 08:17:57 +0200
> > From: "T.A.Wassenaar" <T.A.Wassenaar at rug.nl>
> > Subject: Re: [gmx-users] cell output
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <web-4555627 at mail3.rug.nl>
> > Content-Type: text/plain; charset="ISO-8859-1"; format="flowed"
> >
> >
> > You can ofcourse also write your trajectory as a .pdb file
> > (with a selection of 1 atom, probably, because I think
> > trjconv will complain with empty selections).
> > Then you can extract the parameters with a small script.
> >
> > Tsjerk
> >
> >
> > On Tue, 07 Jun 2005 19:27:09 +0200
> > David <spoel at xray.bmc.uu.se> wrote:
> >> On Tue, 2005-06-07 at 13:07 -0400, Lianqing Zheng wrote:
> >>> Thanks, David! How about these parameters versus time?
> >> In that case you can output the box vectors using
> >>g_energy and apply a
> >> bit of math your self. If you supply the C-code I'm
> >>willing to put it
> >> into g_energy.
> >>
> >>>
> >>> Lianqing
> >>>
> >>>
> >>> On Tue, 7 Jun 2005, David wrote:
> >>>
> >>> >On Tue, 2005-06-07 at 10:27 -0400, Lianqing Zheng
> >>>wrote:
> >>> >> Dear gmx-pals,
> >>> >>
> >>> >> Is there any way to output cell vectors like [a, b,
> >>>c, alpha, beta gamma],
> >>> >> rather than [xx, yx, yy,zx, zy, zz]?
> >>> >Yes, if you store a file as a pdb file.
> >>> >>
> >>> >> Thanks!
> >>> >>
> >>> >> Lianqing
> >>> >>
> >>> >>
> >>> >> _______________________________________________
> >>> >> 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.
> >>> >--
> >>> >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://xray.bmc.uu.se/~spoel
> >>> >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>> >
> >>> >_______________________________________________
> >>> >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.
> >>> >
> >>>
> >>> _______________________________________________
> >>> 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.
> >> --
> >> 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://xray.bmc.uu.se/~spoel
> >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>
> >> _______________________________________________
> >> 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.
> >
> >
> >
> > ------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> >
> >
> > End of gmx-users Digest, Vol 14, Issue 26
> > *****************************************
> >
>
>
> _______________________________________________
> 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
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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://xray.bmc.uu.se/~spoel
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