[gmx-users] Re: grompp error message
Luciano
ltcosta at universiabrasil.net
Thu Nov 20 21:12:01 CET 2003
Hi Jodi,
I think that you have check your *.gro and *.top file and to see the
Na+ type. It shouldn't are set correctly.
Cheers,
Luciano
######################################################
Luciano Tavares da Costa
Mestre em Engenharia Química
icq #232852036 ; ltcosta at universiabrasil.net
Doutorando Laboratório de Biofisicoquímica
Instituto de Química - USP
######################################################
----- Mensagem Original -----
De: gmx-users-request at gromacs.org
Data: Quinta, 20 de Novembro de 2003 1:27 pm
Assunto: gmx-users digest, Vol 1 #1098 - 9 msgs
> Send gmx-users mailing list submissions to
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> Today's Topics:
>
> 1. (no subject) (Luca Mollica)
> 2. Re: Could gromacs process RNA? (Luca Mollica)
> 3. Amino terminus atom types (Lieven Buts)
> 4. grompp error message (Jodi Fangman)
> 5. Re: Amino terminus atom types (David van der Spoel)
> 6. RE: LJ-14 default..... (Henrik Rundgren)
> 7. g_rms g_dipole (parinald at unsl.edu.ar)
> 8. Performance (ehab at biof.ufrj.br)
> 9. Re: Performance (Ran Friedman)
>
> --__--__--
>
> Message: 1
> Date: Thu, 20 Nov 2003 11:35:38 +0100
> From: Luca Mollica <mollica.luca at hsr.it>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] (no subject)
> Reply-To: gmx-users at gromacs.org
>
> > Message: 8
> > From: "wang chuanming" <chuanmingwang at hotmail.com>
> > To: gmx-users at gromacs.org
> > Date: Thu, 20 Nov 2003 16:47:05 +0800
> > Subject: [gmx-users] Could gromacs process RNA?
> > Reply-To: gmx-users at gromacs.org
> >
> > Dear all,
> > I have noticed that most works using gromacs were related to
> proteins or
> > lipids. Are there anyone use it for research on RNA? There are
> very few
> > building block in the ff***.rtp or .itp files, I think. Maybe
> users must
> > set up their block and it is difficult for me.
>
> Dear Wang,
>
> I'm not an expert using GROMACS for nucleic acids simulation,
> because
> I'm interested in proteins and lipids, like most of the
> users....but, a
> general rule that must be adopted in analysing a new problem in
> GROMACS,
> according to my opinion and experience, is that the user must build
> a
> new topology for every molecule except protein that he/she will
> have to
> use in the simulation. Also lipids are not by default included in
> GROMACS, but other users have built FF including parameters for
> lipids,
> and topologies .itp files as well.
> This site could be very helpful, please try to use it, and you will
> discover some insights in creating topologies:
>
> http://davapc1.bioch.dundee.ac.uk/prodrg/
>
> The Dundee PRODRG server is a free server that builds topologies
> for
> molecules provided by the user.
> But also search for advices in the whole mailing list and
> topologies and
> force fields all over the web.
>
>
> And MD of RNA usually needs
> > to add ion in the SOL, how can I do it?
>
> It depends on HOW MANY ions do you need: e.g., if your system has a
> global charge of +3, you will have to replace 3 molecules of
> solvent
> with three Cl(-) ions. In this case, you will add in your topology
> file
> the line
>
> #include"ions.itp"
>
> and the final part of topology file
>
> [ molecules ]
> ; Compound #mols
> Protein 1
> SOL 1200
>
> will become as follows:
>
> [ molecules ]
> ; Compound #mols
> Protein 1
> SOL 1197
> CL 3
>
>
>
> Good luck, and enjoy MD!
>
> L
>
>
>
> > Expecting your reply
> > Thanks in advance!
> >
>
>
>
> --__--__--
>
> Message: 2
> Date: Thu, 20 Nov 2003 11:37:24 +0100
> From: Luca Mollica <mollica.luca at hsr.it>
> To: GROMACS mailing list <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Could gromacs process RNA?
> Reply-To: gmx-users at gromacs.org
>
> > Message: 8
> > From: "wang chuanming" <chuanmingwang at hotmail.com>
> > To: gmx-users at gromacs.org
> > Date: Thu, 20 Nov 2003 16:47:05 +0800
> > Subject: [gmx-users] Could gromacs process RNA?
> > Reply-To: gmx-users at gromacs.org
> >
> > Dear all,
> > I have noticed that most works using gromacs were related to
> proteins
> > or lipids. Are there anyone use it for research on RNA? There
> are
> very > few building block in the ff***.rtp or .itp files, I think.
> Maybe > users must set up their block and it is difficult for me.
>
>
> Dear Wang,
>
> I'm not an expert using GROMACS for nucleic acids simulation,
> because
> I'm interested in proteins and lipids, like most of the
> users....but, a
> general rule that must be adopted in analysing a new problem in
> GROMACS,
> according to my opinion and experience, is that the user must build
> a
> new topology for every molecule except protein that he/she will
> have to
> use in the simulation. Also lipids are not by default included in
> GROMACS, but other users have built FF including parameters for
> lipids,
> and topologies .itp files as well.
> This site could be very helpful, please try to use it, and you will
> discover some insights in creating topologies:
>
> http://davapc1.bioch.dundee.ac.uk/prodrg/
>
> The Dundee PRODRG server is a free server that builds topologies
> for
> molecules provided by the user.
> But also search for advices in the whole mailing list and
> topologies and
> force fields all over the web.
>
>
> > And MD of RNA usually needs
> > to add ion in the SOL, how can I do it?
>
>
> It depends on HOW MANY ions do you need: e.g., if your system has a
> global charge of +3, you will have to replace 3 molecules of
> solvent
> with three Cl(-) ions. In this case, you will add in your topology
> file
> the line
>
> #include"ions.itp"
>
> and the final part of topology file
>
> [ molecules ]
> ; Compound #mols
> Protein 1
> SOL 1200
>
> will become as follows:
>
> [ molecules ]
> ; Compound #mols
> Protein 1
> SOL 1197
> CL 3
>
>
>
> Good luck, and enjoy MD!
>
> L
>
>
>
> > Expecting your reply
> > Thanks in advance!
> >
>
>
>
>
*******************************************************************************************************
>
> Luca Mollica
> Dulbecco Telethon Institute (Protein Structure Laboratory)
>
> DIBIT-HSR,Via Olgettina 58
> 20132 Milano (Italy)
>
> Tel: 0039-02-26434824
> Fax: 0039-02-26434813
> E-mail: mollica.luca at hsr.it
>
> DTI website: http://www.telethon.it/dti/
>
>
> --__--__--
>
> Message: 3
> From: Lieven Buts <lieven at ultr.vub.ac.be>
> Organization: Vrije Universiteit Brussel - ULTR
> To: gmx-users at gromacs.org
> Date: Thu, 20 Nov 2003 13:55:07 +0100
> Subject: [gmx-users] Amino terminus atom types
> Reply-To: gmx-users at gromacs.org
>
> I am trying a simple simulation of a protein in water using the
> OPSL-AA force
> field in Gromacs 3.1.4. The N terminus looks like this in the
> topology file:
>
> ----------------------------
> ; Include forcefield parameters
> #include "ffoplsaa.itp"
>
> [ moleculetype ]
> ; Name nrexcl
> Protein_B 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB
> chargeB massB
> 1 MNH3 1 GLN MN1 1 0 8.51535
> 2 MNH3 1 GLN MN2 1 0 8.51535
> 3 opls_287 1 GLN N 1 -0.3 0
> 4 opls_290 1 GLN H1 1 0.33 0
>
> 5 opls_290 1 GLN H2 1 0.33 0
>
> 6 opls_290 1 GLN H3 1 0.33 0
>
> 7 opls_293B 1 GLN CA 2 0.25 13.019
>
> ...
> ----------------------------
>
> Energy minimization works fine, but when I start a position-
> restrained run, I
> get these LINCS warnings:
>
> ----------------------------
> Step 7, time 0.014 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.000000 (between atoms 1 and 2) rms nan
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> ----------------------------
>
> at every step.
>
> Is this a problem?
>
>
>
> Cheers,
>
> --
> Lieven Buts
> Department of Ultrastructure
> Vrije Universiteit Brussel
>
>
> --__--__--
>
> Message: 4
> Date: Thu, 20 Nov 2003 07:20:02 -0600
> From: Jodi Fangman <jodi-fangman at uiowa.edu>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] grompp error message
> Reply-To: gmx-users at gromacs.org
>
> David
> Here is the full grompp output including the error.
> Jodi
>
> grompp -v -f em -c salt -o salt_em -p 1ubq
>
> creating statusfile for 1 node...
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#
> Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
> checking input for internal consistency...
> calling /usr/bin/cpp...
> processing topology...
> Generated 241860 of the 241860 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 241860 of the 241860 1-4 parameter combinations
> Excluding 3 bonded neighbours for Protein 1
> Excluding 2 bonded neighbours for SOL 4513
> Cleaning up temporary file grompp000318
> Fatal error: No such moleculetype NA+
>
>
> --__--__--
>
> Message: 5
> Subject: Re: [gmx-users] Amino terminus atom types
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> To: gmx-users at gromacs.org
> Organization:
> Date: 20 Nov 2003 14:26:41 +0100
> Reply-To: gmx-users at gromacs.org
>
> On Thu, 2003-11-20 at 13:55, Lieven Buts wrote:
> > I am trying a simple simulation of a protein in water using the
> OPSL-AA force
> > field in Gromacs 3.1.4. The N terminus looks like this in the
> topology file:
> >
> > ----------------------------
> > ; Include forcefield parameters
> > #include "ffoplsaa.itp"
> >
> > [ moleculetype ]
> > ; Name nrexcl
> > Protein_B 3
> >
> > [ atoms ]
> > ; nr type resnr residue atom cgnr charge
> mass typeB
> > chargeB massB
> > 1 MNH3 1 GLN MN1 1 0
> 8.51535
> > 2 MNH3 1 GLN MN2 1 0
> 8.51535
> > 3 opls_287 1 GLN N 1 -0.3
> 0
> > 4 opls_290 1 GLN H1 1 0.33
> 0
> > 5 opls_290 1 GLN H2 1 0.33
> 0
> > 6 opls_290 1 GLN H3 1 0.33
> 0
> > 7 opls_293B 1 GLN CA 2 0.25
> 13.019
> > ...
> > ----------------------------
> >
> > Energy minimization works fine, but when I start a position-
> restrained run, I
> > get these LINCS warnings:
> >
> > ----------------------------
> > Step 7, time 0.014 (ps) LINCS WARNING
> > relative constraint deviation after LINCS:
> > max 0.000000 (between atoms 1 and 2) rms nan
> > bonds that rotated more than 30 degrees:
> > atom 1 atom 2 angle previous, current, constraint length
> > ----------------------------
> >
> > at every step.
> >
> > Is this a problem?
> yes,
>
> I'm working on it.
>
> >
> >
> >
> > Cheers,
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assist. 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: Thu, 20 Nov 2003 14:39:32 +0100
> From: Henrik Rundgren <henrik at physc.su.se>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] RE: LJ-14 default.....
> Reply-To: gmx-users at gromacs.org
>
> This is a multi-part message in MIME format.
> --------------090404090709020205060702
> Content-Type: text/plain; charset=us-ascii; format=flowed
> Content-Transfer-Encoding: 7bit
>
> -- __--__-- Message: 7 Subject: Re: [gmx-users] Help: No default
> LJ-14...
> From: David van der Spoel <spoel at xray.bmc.uu.se> To:
> gmx-users at gromacs.org Organization: Date: 20 Nov 2003 09:07:41
> +0100
> Reply-To: gmx-users at gromacs.org On Thu, 2003-11-20 at 09:00, Henrik
> Rundgren wrote:
>
> >> hello all.
> >> I have a problem.
> >> I have run some simulations with Gromacs, and all seems fine.
> >> No I try to run a small peptide in wter, and I get the following
> warnings:>>
> >> Generated 1179 of the 1378 non-bonded parameter combinations
> >> WARNING 1 [file "top.top", line 86]:
> >> No default LJ-14 types, using zeroes
> >> WARNING 2 [file "top.top", line 87]:
> >> No default LJ-14 types, using zeroes
> >> WARNING 3 [file "top.top", line 88]:
> >> No default LJ-14 types, using zeroes
> >> WARNING 4 [file "top.top", line 109]:
> >> No default LJ-14 types, using zeroes
> >> WARNING 5 [file "top.top", line 110]:
> >> No default LJ-14 types, using zeroes
> >> WARNING 6 [file "top.top", line 111]:
> >> No default LJ-14 types, using zeroes
> >> Excluding 3 bonded neighbours for Protein 1
> >> Excluding 2 bonded neighbours for SOL 884
> >>
> >> Then it continues and makes the infile .trp, but I doubt that
> this is ok
> >> to run an simulation on....
> >> I have checked in the topology file, and the default type value
> is 1
> >> (=LJ)... so I don't see where this warning is coming from.
> >>
> >have you checked which atom pair is listed in top.top lines 86,
> 87, 88,
> >109-111
> >
> >
> >
> >>> thanks for the help.
> >>> sincerely,
> >>> henrik
> >>
> >>
> > -- David.
> >
> ________________________________________________________________________
> > David van der Spoel, PhD, Assist. 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
> >
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>
>
>
> Hello,
> Yes, I have looked in it.. but I can't understand why it would want
> to
> use the ZN: or SI: or NA:pairs in the topology file... since I
> haven't
> defined any "metals" in the pdb file (it's just a basic dipeptide
> of ALA
> ZW-form).
> I have missed some basics here... shouldn't the topology only
> include
> the atoms defined from the pdb file's?
> (I used your spc216 file for water though. but that one seems ok
> when
> looking at it...)
>
> From top.top following can be read...
>
> [ nonbond_params ]
> line ; i j func c6 c12
> 86 O NL 1 0.23473E-02 0.34518E-05
> 87 O NR5* 1 0.23473E-02 0.20711E-05
> 88 O ZN 1 0.00000E+00 0.10931E-06
> 109 OM NR6* 1 0.23473E-02 0.33890E-05
> 110 OM SI 1 0.57734E-02 0.86722E-05
> 111 OM NA 1 0.40370E-03 0.44478E-06
>
> thanks for input.
> henrik
>
> --
> _________________________________________________________________
> Henrik Rundgren
> Division of Physical Chemistry
> Arrhenius Laboratory
> Stockholm University
> S-106 91 Stockholm
> Sweden
>
> E-mail: Henrik at physc.su.se
> Telephone: +46-(0)8-16 12 63
> Fax: +46-(0)8-15 21 87
> Website: www.fos.su.se/~henrik
> _________________________________________________________________
>
>
> --------------090404090709020205060702
> Content-Type: text/html; charset=us-ascii
> Content-Transfer-Encoding: 7bit
>
> <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
> <html>
> <head>
> <meta http-equiv="Content-Type" content="text/html;charset=ISO-
> 8859-1">
> <title></title>
> </head>
> <body>
> <pre wrap=""><div class="moz-txt-sig"><div class="moz-txt-sig">--
> __--__--
>
> Message: 7
> Subject: Re: [gmx-users] Help: No default LJ-14...
> From: David van der Spoel
> href="mailto:spoel at xray.bmc.uu.se"><spoel at xray.bmc.uu.se>To:
> href="mailto:gmx-users at gromacs.org">gmx-users at gromacs.org
> Organization:
> Date: 20 Nov 2003 09:07:41 +0100
> Reply-To: href="mailto:gmx-users at gromacs.org">gmx-users at gromacs.org
>
> On Thu, 2003-11-20 at 09:00, Henrik Rundgren wrote:
> </div></div></pre>
> <blockquote type="cite">
> <pre wrap=""><span class="moz-txt-citetags">> </span>hello all.
> <span class="moz-txt-citetags">> </span>I have a problem.
> <span class="moz-txt-citetags">> </span>I have run some
> simulations with Gromacs, and all seems fine.
> <span class="moz-txt-citetags">> </span>No I try to run a small
> peptide in wter, and I get the following warnings:
> <span class="moz-txt-citetags">> </span>
> <span class="moz-txt-citetags">> </span> Generated 1179 of the
> 1378 non-bonded parameter combinations
> <span class="moz-txt-citetags">> </span>WARNING 1 [file
> "top.top", line 86]:
> <span class="moz-txt-citetags">> </span> No default LJ-14
> types, using zeroes
> <span class="moz-txt-citetags">> </span>WARNING 2 [file
> "top.top", line 87]:
> <span class="moz-txt-citetags">> </span> No default LJ-14
> types, using zeroes
> <span class="moz-txt-citetags">> </span>WARNING 3 [file
> "top.top", line 88]:
> <span class="moz-txt-citetags">> </span> No default LJ-14
> types, using zeroes
> <span class="moz-txt-citetags">> </span>WARNING 4 [file
> "top.top", line 109]:
> <span class="moz-txt-citetags">> </span> No default LJ-14
> types, using zeroes
> <span class="moz-txt-citetags">> </span>WARNING 5 [file
> "top.top", line 110]:
> <span class="moz-txt-citetags">> </span> No default LJ-14
> types, using zeroes
> <span class="moz-txt-citetags">> </span>WARNING 6 [file
> "top.top", line 111]:
> <span class="moz-txt-citetags">> </span> No default LJ-14
> types, using zeroes
> <span class="moz-txt-citetags">> </span>Excluding 3 bonded
> neighbours for Protein 1
> <span class="moz-txt-citetags">> </span>Excluding 2 bonded
> neighbours for SOL 884
> <span class="moz-txt-citetags">> </span>
> <span class="moz-txt-citetags">> </span>Then it continues and
> makes the infile .trp, but I doubt that this is ok
> <span class="moz-txt-citetags">> </span>to run an simulation on....
> <span class="moz-txt-citetags">> </span>I have checked in the
> topology file, and the default type value is 1
> <span class="moz-txt-citetags">> </span>(=LJ)... so I don't see
> where this warning is coming from.
> <span class="moz-txt-citetags">> </span><!---->
> have you checked which atom pair is listed in top.top lines 86, 87,
> 88,109-111
>
> </pre>
> <blockquote type="cite">
> <pre wrap=""><span class="moz-txt-citetags">> </span>thanks
> for the help.
> <span class="moz-txt-citetags">> </span>sincerely,
> <span class="moz-txt-citetags">> </span>henrik
> </pre>
> </blockquote>
> <!---->
> <div class="moz-txt-sig">-- David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assist. 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 href="mailto:spoel at xray.bmc.uu.se">spoel at xray.bmc.uu.se <a
> class="moz-txt-link-abbreviated"
> href="mailto:spoel at gromacs.org">spoel at gromacs.org <a
> class="moz-txt-link-freetext"
> href="http://xray.bmc.uu.se/%7Espoel">"
target="l">http://xray.bmc.uu.se/~spoel
>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
</div>
> <pre wrap=""></pre>
> </blockquote>
> <pre wrap=""><!---->
> </pre>
> <br>
> Hello,<br>
> Yes, I have looked in it.. but I can't understand why it would want to
> use the ZN: or SI: or NA:pairs in the topology file... since I haven't
> defined any "metals" in the pdb file (it's just a basic dipeptide of
> ALA ZW-form). <br>
> I have missed some basics here... shouldn't the topology only include
> the atoms defined from the pdb file's?<br>
> (I used your spc216 file for water though. but that one seems ok when
> looking at it...)<br>
> <br>
> From top.top following can be read...<br>
> <br>
> [ nonbond_params ]<br>
> line ; i j func c6 c12<br>
> 86 O NL 1 0.23473E-02 0.34518E-05<br>
> 87 O NR5* 1 0.23473E-02 0.20711E-05<br>
> 88 O ZN 1 0.00000E+00 0.10931E-06<br>
> 109 OM NR6* 1 0.23473E-02 0.33890E-05<br>
> 110 OM SI 1 0.57734E-02 0.86722E-05<br>
> 111 OM NA 1 0.40370E-03 0.44478E-06<br>
> <br>
> thanks for input.<br>
> henrik<br>
> <pre class="moz-signature" cols="72">--
> _________________________________________________________________
> Henrik Rundgren
> Division of Physical Chemistry
> Arrhenius Laboratory
> Stockholm University
> S-106 91 Stockholm
> Sweden
>
> E-mail: Henrik at physc.su.se
> Telephone: +46-(0)8-16 12 63
> Fax: +46-(0)8-15 21 87
> Website: http://www.fos.su.se/~henrik">www.fos.su.se/~henrik
> _________________________________________________________________
> </pre>
> </body>
> </html>
>
> --------------090404090709020205060702--
>
>
> --__--__--
>
> Message: 7
> Date: Thu, 20 Nov 2003 10:42:57 -0300 (ART)
> From: <parinald at unsl.edu.ar>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] g_rms g_dipole
> Reply-To: gmx-users at gromacs.org
>
> Hello again:
>
> sorry, I was not expresed correctly :
>
> The file aver.xvg (of g_dipole) contains <|M|^2/N> and <|M|>^2/N,
> what the
> > meaning of <|M|>^2 / <|M|^2> ? what is N?.
>
> Thank you. I must return to the question RMSD in estructure:
> in this problem, what is reference estructure?
> is better to use g_rmsdist?( where the distance Rij between atoms
> at time t
> is compared with the distance between the same atoms at time 0).
> Pablo.
>
>
>
> --__--__--
>
> Message: 8
> Date: Thu, 20 Nov 2003 14:54:38 +0000
> From: ehab at biof.ufrj.br
> To: GROMACS mailing list <gmx-users at gromacs.org>
> Subject: [gmx-users] Performance
> Reply-To: gmx-users at gromacs.org
>
> Hi all,
> Please, somebody can tell me how is the time performance of GROMACS
> in a
> Origin 2000? I just need to know the system size, the time of the
> simulation(like 1ns) and the real time it took to run (like 3 days)
> on this machine.
>
> Thanks in advance,
>
> Elza
>
>
> *************************************
> Ludwig Institute for Cancer Research
> Computational Biology Lab
> Sao Paulo-SP - Brazil
>
> --__--__--
>
> Message: 9
> Date: Thu, 20 Nov 2003 17:26:24 +0200
> From: Ran Friedman <ran at hemi.tau.ac.il>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Performance
> Reply-To: gmx-users at gromacs.org
>
>
> --------------54406773AE687C61903E147E
> Content-Type: text/plain; charset=us-ascii
> Content-Transfer-Encoding: 7bit
>
> Hi,
>
> Rough data:
>
> 1ns simulation of ~22,000 atoms on 8cpu (R12000, 400MHZ) with the
> gromacs FF, with PME, time step 2fs, takes me 44-48 hours.
>
> Ran.
>
> ehab at biof.ufrj.br wrote:
>
> > Hi all,
> > Please, somebody can tell me how is the time performance of
> GROMACS in a
> > Origin 2000? I just need to know the system size, the time of the
> simulation> (like 1ns) and the real time it took to run (like 3
> days) on this machine.
> >
> > Thanks in advance,
> >
> > Elza
> >
> > *************************************
> > Ludwig Institute for Cancer Research
> > Computational Biology Lab
> > Sao Paulo-SP - Brazil
> > _______________________________________________
> > 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.
>
> --
> ------------------------------------------------------
> Ran Friedman
> Laser laboratory for fast reactions in biology
> Department of biochemistry
> Faculty of life sciences
> Tel-Aviv university
> 972-3-6409824
> ------------------------------------------------------
>
>
>
> --------------54406773AE687C61903E147E
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> Content-Transfer-Encoding: 7bit
>
> <!doctype html public "-//w3c//dtd html 4.0 transitional//en">
> <html>
>
> <pre>Hi,</pre>
>
> <pre></pre>
>
> <pre>Rough data:</pre>
>
> <pre>1ns simulation of ~22,000 atoms on 8cpu (R12000, 400MHZ) with
> the gromacs FF, with PME, time step 2fs, takes me 44-48 hours.</pre>
>
> <pre></pre>
>
> <pre>Ran.</pre>
>
> <pre></pre>
> ehab at biof.ufrj.br wrote:
> <blockquote TYPE=CITE>Hi all,
> <br>Please, somebody can tell me how is the time performance of
> GROMACSin a
> <br>Origin 2000? I just need to know the system size, the time of
> the simulation
> <br>(like 1ns) and the real time it took to run (like 3 days) on
> this machine.
> <p>Thanks in advance,
> <p>Elza
> <p>*************************************
> <br>Ludwig Institute for Cancer Research
> <br>Computational Biology Lab
> <br>Sao Paulo-SP - Brazil
> <br>_______________________________________________
> <br>gmx-users mailing list
> <br>gmx-users at gromacs.org
> <br>http://www.gromacs.org/mailman/listinfo/gmx-users">"
> target="l">http://www.gromacs.org/mailman/listinfo/gmx-users
> <br>Please don't post (un)subscribe requests to the list. Use the
> <br>www interface or send it to gmx-users-
> request at gromacs.org.</blockquote>
> <pre>--
> ------------------------------------------------------
> Ran Friedman
> Laser laboratory for fast reactions in biology
> Department of biochemistry
> Faculty of life sciences
> Tel-Aviv university
> 972-3-6409824
> ------------------------------------------------------</pre>
> </html>
>
> --------------54406773AE687C61903E147E--
>
>
>
> --__--__--
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
>
>
> End of gmx-users Digest
>
------------------------------------------------------------------------
Vote no Universia para o Prêmio IBest 2004 e concorra a uma
viagem para Trancoso.
www.universiabrasil.net
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