[gmx-users] Grompp error (no default RB dihedral)
Lakhani, Ahmed Ashiqali
aalakhan at uic.edu
Sat Jun 11 00:06:18 CEST 2005
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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.
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> Today's Topics:
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> 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
>>
>> _______________________________________________
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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.
>> >
>>
>> _______________________________________________
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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.
>
>
>> _______________________________________________
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>> 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: 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.
>
>
>
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