[gmx-users] Re: gmx-users Digest, Vol 64, Issue 156
DreamCatcher
huangshuping1987 at gmail.com
Tue Aug 25 03:34:33 CEST 2009
Dear Justin,
I did make the rtp and hdb files in accordance with the tutorial
onthe website
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html<http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html,but>
,but <http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html>the
problem cann't be settle,what can I do?
Looking forward for your reply!
Thanks,
dreamcatcher
On Tue, Aug 25, 2009 at 2:57 AM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. Re: [Fwd: Please solve my problem] (cesteban at unsl.edu.ar)
> 2. Something about getting started (DreamCatcher)
> 3. Re: Something about getting started (Justin A. Lemkul)
> 4. Re: correlation function (Jamie Seyed)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 24 Aug 2009 10:30:45 -0400 (ARGSL-DT)
> From: cesteban at unsl.edu.ar
> Subject: Re: [gmx-users] [Fwd: Please solve my problem]
> To: jalemkul at vt.edu, "Discussion list for GROMACS users"
> <gmx-users at gromacs.org>
> Message-ID:
> <51938.64.76.125.131.1251124245.squirrel at webmail2.unsl.edu.ar>
> Content-Type: text/plain;charset=iso-8859-1
>
> Hi again
> the MPI coding is OPEN MPI 1.2.7 that is found in the ROCKS CLUSTER 5.1
> distribution
> thanks
> Carmen
> >
> > cesteban at unsl.edu.ar wrote:
> >> Hi All
> >> I have similar problem using gromacs 4.0.2.
> >> The MD simulation (5 ns) on single processor is complited in 5 days, but
> >> the same MD can`t be complited on cluster on 4 or 8 processors. The MD
> >> simulation is stopped without any error message.
> >> Any help would be appreciated
> >
> > Which MPI implementation are you using? Some are known to be buggy.
> > Also, to
> > rule out any other potentially buggy behavior, upgrade to version 4.0.5;
> > 4.0.2
> > is several months old.
> >
> > -Justin
> >
> >> Carmen
> >>> To,
> >>> David van der Spoel
> >>>
> >>> Dear Sir,
> >>>
> >>> I am using Gromacs 3.2.1 for the MD simulation on clusters but facing a
> >>> problem.
> >>> I am giving job for 500000 steps step size 0.002ps (total 1ns) but my
> >>> job is stopped after 470000 steps. when i run this on 4 processors.
> >>>
> >>> But the same job is completed on 2 processors.Why this happing i am not
> >>> able to understand.
> >>>
> >>> Another thing is that job for 1500000 steps step size 0.002ps (total
> >>> 3ns) is stopped after 375000 steps on 2 processors
> >>> and after 587000 steps on 4 processors, without any error message.
> >>>
> >>> What could be the problem and how to solve it, please help me.
> >>>
> >>> even i tried the 2 same jobs for 1000000 steps step size 0.002ps (total
> >>> 2ns), one on single processor it is completed in 8 days
> >>> but the same job is stop after 550000 steps on 4 processors.
> >>>
> >>> Is there any change is required in MPI coding or in .mdp files. Sir if
> >>> you need any other please let me know.
> >>>
> >>> Please solve my problem, I will be highly obliged.
> >>>
> >>>
> >>> DvdS:
> >>>
> >>> Please upgrade to a recent version. 3.2.1 is more than five years old.
> >>>
> >>>
> >>>
> >>> With warm regards.
> >>> Shikhar
> >>>
> >>>
> >>>
> >>> --
> >>> ------------------------------------------------------------
> >>> Shikhar Gupta
> >>> Senior Research Fellow
> >>> Pharmacoinformatics Department
> >>> Block- A (Room No.- 208)
> >>> National Institute of Pharmaceutical Education & Research( NIPER )
> >>> Sec- 67, S.A.S Nagar
> >>> Mohali, Punjab (India)
> >>> Web-Site: www.niper.ac.in <http://www.niper.ac.in>
> >>> PIN- 160062
> >>> Email:shik_sun at rediffmail.com <Email%3Ashik_sun at rediffmail.com>
> >>> <mailto:Email%3Ashik_sun at rediffmail.com<Email%253Ashik_sun at rediffmail.com>
> >,shiksun at gmail.com
> >>> <mailto:shiksun at gmail.com>
> >>>
> >>>
> >>>
> >>>
> >>> --
> >>> ------------------------------------------------------------
> >>> Shikhar Gupta
> >>> Senior Research Fellow
> >>> Pharmacoinformatics Department
> >>> Block- A (Room No.- 208)
> >>> National Institute of Pharmaceutical Education & Research( NIPER )
> >>> Sec- 67, S.A.S Nagar
> >>> Mohali, Punjab (India)
> >>> Web-Site: www.niper.ac.in <http://www.niper.ac.in>
> >>> PIN- 160062
> >>> Email:shik_sun at rediffmail.com <Email%3Ashik_sun at rediffmail.com>
> >>> <mailto:Email%3Ashik_sun at rediffmail.com<Email%253Ashik_sun at rediffmail.com>
> >,shiksun at gmail.com
> >>> <mailto:shiksun at gmail.com>
> >>>
> >>>
> >>> --
> >>> David van der Spoel, Ph.D., Professor of Biology
> >>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
> >>> University.
> >>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax:
> +4618511755.
> >>> 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://lists.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
> >>>
> >>
> >>
> >> _______________________________________________
> >> gmx-users mailing list gmx-users at gromacs.org
> >> http://lists.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
> >>
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.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
> >
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 25 Aug 2009 00:04:26 +0800
> From: DreamCatcher <huangshuping1987 at gmail.com>
> Subject: [gmx-users] Something about getting started
> To: gmx-users at gromacs.org
> Message-ID:
> <4eaf737d0908240904i69e38267mde46802714ce484e at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear gmx-users,
> I am a freshman of gmx and I wanna use gromacs for polyvinyl-alcohol
> simulation.But I don't even know how to start it.
> Is it necessary to start my simulation with a .pdb files?If so,What
> should I do before this?I can make an pdb file for a chain of syndiotatic
> polyvinyl-alcohols via Material Studio or some other packages,but the
> residue cann't be recognize,so I have to modify some top files to correct
> it.I just modify the .hdb and rtp files endeavor to make it.But it seems
> not
> an easy work.
> the message the package sent to me is as follows,appreciate if somebody
> can help me to handle this!
> *** (this is an previous version.when i try to use pdb2gmx to get its .top
> file,a fatal error reminds:
> "source code file : resall.c line:279 ()
> Fatal errors:
> in .rtp file at line : "
> when I add the charge and chargegroupndx of the atoms,there comes a
> similar error ):
> My attempt is as follows:
> ### in rtp file
> [ VAB ]
> [ atoms ]
> CB opls_135
> HB1 opls_140
> HB2 opls_140
> HB3 opls_140
> CA opls_158
> HA1 opls_140
> OH opls_154
> HO opls_155
>
> [ bonds ]
> CB HB1
> CB HB2
> CB HB3
> CB CA
> CA HA1
> CA OH
> OH HO
> CA +CB
>
> [VA ]
> [ atoms ]
> CB opls_136
> HB1 opls_140
> HB2 opls_140
> CA opls_158
> HA1 opls_140
> OA opls_154
> HOA opls_155
> CG opls_136
> HG1 opls_140
> HG2 opls_140
> CD opls_158
> HD opls_140
> OD opls_154
> HOD opls_155
>
> [ bonds ]
> CB -CA
> CB HB1
> CB HB2
> CB CA
> CA HA1
> CA OH
> OH HO
> CA CG
> CG HG1
> CG HG2
> CG CD
> CD HD
> CD OD
> OD HOD
> CD +CB
>
> [VAE]
> [ atoms ]
> CB opls_136
> HB1 opls_140
> HB2 opls_140
> CA opls_157
> HA1 opls_140
> HA2 opls_140
> OH opls_154
> HO opls_155
>
> [ bonds ]
> CB -CD
> CB HB1
> CB HB2
> CB CA
> CA HA1
> CA HA2
> CA OH
> OH HO
>
> #### in .hdb file:
> ; H add type H i j k
> VAB 3
> 3 4 HB CB CA +CB
> 1 5 HA CA CB +CB
> 1 2 HO OH CA +CB
> VA 6
> 2 6 HB CB CA -CA
> 1 5 HA CA CB CG
> 1 2 HOA OA CA CG
> 2 6 HG CG CA CD
> 1 5 HD CD CG +CB
> 1 1 HOD OD CD CG
> VAE 3
> 2 6 HB CB CA -CD
> 2 6 HA CA CB +CB
> 1 2 HO OH CA +CB
> -------------- next part --------------
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> ------------------------------
>
> Message: 3
> Date: Mon, 24 Aug 2009 12:41:00 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Something about getting started
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4A92C29C.4050206 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> DreamCatcher wrote:
> > Dear gmx-users,
> > I am a freshman of gmx and I wanna use gromacs for
> > polyvinyl-alcohol simulation.But I don't even know how to start it.
>
> Then start simple with some tutorial material:
>
> http://oldwiki.gromacs.org/index.php/Tutorials
>
> > Is it necessary to start my simulation with a .pdb files?If
>
> You need some sort of structure to start with; .pdb files are generally the
> starting point.
>
> > so,What should I do before this?I can make an pdb file for a chain of
> > syndiotatic polyvinyl-alcohols via Material Studio or some other
> > packages,but the residue cann't be recognize,so I have to modify some
> > top files to correct it.I just modify the .hdb and rtp files endeavor to
> > make it.But it seems not an easy work.
>
> Indeed, it is not. I again suggest you start with some basic tutorials
> with
> robust systems so you learn the workflow of a Gromacs simulation. Once
> you've
> got a handle on how everything flows, then attempt your system.
>
> For polymers, you may find this thread useful:
>
> http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html
>
> -Justin
>
> > the message the package sent to me is as follows,appreciate if
> > somebody can help me to handle this!
> > *** (this is an previous version.when i try to use pdb2gmx to get its
> > .top file,a fatal error reminds:
> > "source code file : resall.c line:279 ()
> > Fatal errors:
> > in .rtp file at line : "
> > when I add the charge and chargegroupndx of the atoms,there comes a
> > similar error ):
> > My attempt is as follows:
> > ### in rtp file
> > [ VAB ]
> > [ atoms ]
> > CB opls_135
> > HB1 opls_140
> > HB2 opls_140
> > HB3 opls_140
> > CA opls_158
> > HA1 opls_140
> > OH opls_154
> > HO opls_155
> >
> > [ bonds ]
> > CB HB1
> > CB HB2
> > CB HB3
> > CB CA
> > CA HA1
> > CA OH
> > OH HO
> > CA +CB
> >
> > [VA ]
> > [ atoms ]
> > CB opls_136
> > HB1 opls_140
> > HB2 opls_140
> > CA opls_158
> > HA1 opls_140
> > OA opls_154
> > HOA opls_155
> > CG opls_136
> > HG1 opls_140
> > HG2 opls_140
> > CD opls_158
> > HD opls_140
> > OD opls_154
> > HOD opls_155
> >
> > [ bonds ]
> > CB -CA
> > CB HB1
> > CB HB2
> > CB CA
> > CA HA1
> > CA OH
> > OH HO
> > CA CG
> > CG HG1
> > CG HG2
> > CG CD
> > CD HD
> > CD OD
> > OD HOD
> > CD +CB
> >
> > [VAE]
> > [ atoms ]
> > CB opls_136
> > HB1 opls_140
> > HB2 opls_140
> > CA opls_157
> > HA1 opls_140
> > HA2 opls_140
> > OH opls_154
> > HO opls_155
> >
> > [ bonds ]
> > CB -CD
> > CB HB1
> > CB HB2
> > CB CA
> > CA HA1
> > CA HA2
> > CA OH
> > OH HO
> >
> > #### in .hdb file:
> > ; H add type H i j k
> > VAB 3
> > 3 4 HB CB CA +CB
> > 1 5 HA CA CB +CB
> > 1 2 HO OH CA +CB
> > VA 6
> > 2 6 HB CB CA -CA
> > 1 5 HA CA CB CG
> > 1 2 HOA OA CA CG
> > 2 6 HG CG CA CD
> > 1 5 HD CD CG +CB
> > 1 1 HOD OD CD CG
> > VAE 3
> > 2 6 HB CB CA -CD
> > 2 6 HA CA CB +CB
> > 1 2 HO OH CA +CB
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.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
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 24 Aug 2009 14:57:39 -0400
> From: Jamie Seyed <jamie.seyed at gmail.com>
> Subject: Re: [gmx-users] correlation function
> To: jalemkul at vt.edu, Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID:
> <a9e5cd7b0908241157l69130530j6cfaf4e896ef0da4 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On Sun, Aug 23, 2009 at 7:32 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> >
> > Actually when I open autocorr.xvg I can see from data/feature
> >> extraction/ the last set is S1295 (N=101, autocorr.xvg) which means
> >> they are 1296 graphs each with poor statistics start at 1 and coming
> >> down. To have a ACF for a system I expect to get one graph with good
> >> statistic... I hope I make it clear now.
> >>
> >
> > What did you extract with g_traj? All the coordinates of all the
> > molecules? The command line you gave would be helpful here. It would
> seem
> > that 1296/216 = 6, therefore (and this is just a guess) then g_analyze is
> > trying to calculate some sort of ACF between all coordinates: x-x, y-y,
> z-z,
> > x-y, x-z, y-z. That way, you'd be getting these ACF's for each
> individual
> > molecule. Again, just a guess.
>
>
> Hi Justin,
> I think that I extract only the coordinates for my desired atoms using this
> command:
> g_traj -f f.xtc -s f.tpr -n f.ndx -ox coord.xvg
> and then
> g_analyze -f coord.xvg -ac autocorr.xvg
>
> Is that the way to get ACF or I am doing something wrong here?? Many Thanks
> in Advance/Jamie
>
>
> >
> >
> > -Justin
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.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
> >
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> gmx-users at gromacs.org
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>
> End of gmx-users Digest, Vol 64, Issue 156
> ******************************************
>
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