[gmx-users] xpm2ps help
Justin A. Lemkul
jalemkul at vt.edu
Tue Apr 15 16:57:05 CEST 2008
Quoting "Rigden, LucianeVMello" <Luciane.Rigden at liverpool.ac.uk>:
> Dear all,
>
> I am working with gromacs 3.3.3
>
> Trying to analyse possible changes in the secondary structure of the peptide
> along the simulation.
>
> do_dssp -f traj.xtc -s topol.tpr -sc -dt 5
> 1 protein
I believe the proper analysis should be done on Group 5, 'MainChain.' Probably
xpm2ps cannot process the dssp output if you've analyzed the whole Protein.
-Justin
>
> xpm2ps -f ss.xpm
>
> There are 1 matrices in ss.xpm
> Matrix 0 is 20001 x 12
> zsh: segmentation fault xpm2ps -f ss.xpm
>
>
> Any help?
> if xpm2ps is really a problem, as I had already noticed other people
> complains in the past, is there an alternative way to analyse it?
>
> Thanks in advance for your help.
> Luciane
>
> Dr Luciane Vieira de Mello
> School of Biological Sciences
> Room 2.20, Life Science Building
> Tel:(+44) 151 795 5140
> FAX:(+44) 151 794 5130
> University of Liverpool
> Crown St.,Liverpool L69 7ZB, U.K.
>
>
>
> -----Original Message-----
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> gmx-users-request at gromacs.org
> Sent: Thu 3/13/2008 12:12 AM
> To: gmx-users at gromacs.org
> Subject: gmx-users Digest, Vol 47, Issue 39
>
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> Today's Topics:
>
> 1. Re: trjconv output at a specified time (Liu Shiyong)
> 2. Re: problem with mpi configuration. (Diego Enry)
> 3. Re: trjconv output at a specified time (Alan Dodd)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 12 Mar 2008 18:24:00 -0500
> From: "Liu Shiyong" <liushiyong at gmail.com>
> Subject: Re: [gmx-users] trjconv output at a specified time
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID:
> <c098189c0803121624k47d207b9k8176e9104a16e589 at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Thanks.
>
> The trajectory starts at 125ps ?
>
> So step 1 == 125 ps
> step 2 == 250 ps
> step 3 == 375 ps
>
> Where is 125ps from ?
>
> But
>
> ; RUN CONTROL PARAMETERS
> integrator = steep
> ; Start time and timestep in ps
> tinit = 0
> dt = 0.002
>
>
>
> On Wed, Mar 12, 2008 at 5:32 PM, Alan Dodd <anoddlad at yahoo.com> wrote:
>
> > You asked for the frame at 1ps. The trajectory starts at 125ps, so
> > unsurprisingly the program does not give you an output.
> >
> > ----- Original Message ----
> > From: Liu Shiyong <liushiyong at gmail.com>
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Sent: Wednesday, March 12, 2008 10:07:17 PM
> > Subject: [gmx-users] trjconv output at a specified time
> >
> > Hi,
> >
> > I want to output a structure in a given time, for example , in step 1
> > during minimization.
> >
> > I tried the following command using dump:
> > trjconv -f r-l_1_oplsaa.minim_traj.trr -timestep 1 -o m.pdb -s
> > r-l_1_oplsaa.input.tpr -t0 0 -dump 1
> >
> > But It didnot work.
> >
> > Output msg:
> >
> > Select a group: 2
> > Selected 2: 'Protein-H'
> > trn version: GMX_trn_file (single precision)
> > Reading frame 0 time 125.000
> > Back Off! I just backed up m.pdb to ./#m.pdb.1#
> > Last frame 19 time 2418.000
> >
> > WARNING no output, trajectory ended at 2418
> >
> >
> > gcq#76: "Baseball Heroes Only" (P.J. Harvey)
> >
> > Best
> >
> > --
> > Shiyong Liu
> > Research Assistant
> > center for bioinformatics in the university of kansas
> > Lab: (785)864-1962
> > Email: syliu at ku.edu (shiyongliu at ku.edu or liushiyong at ku.edu)
> > Homepage:
> http://www.people.ku.edu/~syliu<http://www.people.ku.edu/%7Esyliu>
> > Lab: http://vakser.bioinformatics.ku.edu/people
> > Phone: (785) 864-1962
> >
> >
> > -----Inline Attachment Follows-----
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
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> >
>
>
>
> --
> Shiyong Liu
> Research Assistant
> center for bioinformatics in the university of kansas
> Lab: (785)864-1962
> Email: syliu at ku.edu (shiyongliu at ku.edu or liushiyong at ku.edu)
> Homepage: http://www.people.ku.edu/~syliu
> Lab: http://vakser.bioinformatics.ku.edu/people
> Phone: (785) 864-1962
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>
> Message: 2
> Date: Wed, 12 Mar 2008 20:29:24 -0300
> From: "Diego Enry" <diego.enry at gmail.com>
> Subject: Re: [gmx-users] problem with mpi configuration.
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID:
> <eae4cfe70803121629w2122b842ia787d4dc1bc7d316 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> /usr/local/gromacs/bin/grompp_mpi_d--prefix=/usr/local/gromacs333
> <<= just zoom in the middle of the command
>
> right here:
>
> mpi_d--prefix=
>
> you forgot to put a space between "mpi_d" and "--prefix"
>
> copy&paste the corrected version bellow.
> ./configure --enable-mpi --program-suffix=_mpi --prefix=/usr/local/gromacs332
>
> have fun !
>
>
> On Wed, Mar 12, 2008 at 4:05 PM, mario ciappy <mariociap at yahoo.it> wrote:
> >
> > Thank you very much for help me.
> > I have try to install gromacs 3.3.3 on rhel 4.0.
> > I try to configure gromacs single with the command "./configure
> > --enable-mpi --program-suffix=_mpi--prefix=/usr/local/gromacs332", but when
> > I try to install, I have this error:
> > usr/bin/install: cannot create regular file
> > `/usr/local/gromacs/bin/grompp_mpi_d--prefix=/usr/local/gromacs333': No
> such
> > file or directory
> > make[3]: *** [install-binPROGRAMS] Error 1
> > make[3]: Leaving directory `/home/mario/gromacs-3.3.3/src/kernel'
> > make[2]: *** [install-am] Error 2
> > make[2]: Leaving directory `/home/mario/gromacs-3.3.3/src/kernel'
> > make[1]: *** [install-recursive] Error 1
> > make[1]: Leaving directory `/home/mario/gromacs-3.3.3/src'
> > make: *** [install-recursive] Error 1
> > I have try to edit the end of the configure command
> "/usr/local/gromacs332"
> > with"/usr/local/gromacs333" and "/usr/local/gromacs" but I have anlogue
> > errors. Can you help me?
> >
> > Thanks in advance.
> >
> >
> > Mario
> > Diego Enry <diego.enry at gmail.com> ha scritto:
> > You should check the user guide.
> >
> http://www.mcs.anl.gov/research/projects/mpich2/documentation/index.php?s=docs
> >
> > In a nutshell:
> > 1) You need is to install mpich in all machines. Actually you can sync
> > the mpich install directory (also gromacs).
> > 2) You also need to have the same /etc/hosts on every machine. rsync that.
> > 3) You need to grant ssh access without password by creating a rsa-key
> > for every user
> >
> > Fell free to private message if you need any additional help.
> >
> > Ciao.
> >
> > On Tue, Mar 4, 2008 at 6:04 AM, mario ciappy wrote:
> > > Thank's Diego,
> > > I'm grateful to you. I have only one question. How can I configure
> mpi/lam
> > > for relaize the comunication between nodes?
> > > I have created an hostsfile with my ip addresses.
> > > Thank's a lot in advance.
> > >
> > > Mario
> > >
> > > Diego Enry ha scritto:
> >
> >
> > >
> > > Since you didn't show us the problems you met.. try following this:
> > >
> > > #1) Download essential packages
> > > #1.1) mpich
> > > wget
> > >
> >
>
http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/mpich2-1.0.6p1.tar.gz
> > >
> > > #1.2) fftw
> > > wget ftp://ftp.fftw.org/pub/fftw/fftw-3.1.2.tar.gz
> > >
> > > #1.3) gromacs
> > > wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-3.3.2.tar.gz
> > >
> > >
> > > #2) compile packages:
> > >
> > > #2.1) mpich
> > > tar xvfz mpich2-1.0.6p1.tar.gz
> > > cd mpich2-1.0.6p1
> > > make distclean
> > > ./configure --with-device=ch3:nemesis --enable-fast --disable-cxx
> > > --enable-error-checking=no CFLAGS=-O3 FFLAGS=-O3
> > > make
> > > make install
> > > make distclean
> > > cd ..
> > >
> > > #2.2) fftw single
> > > tar xvfz fftw-3.1.2.tar.gz
> > > cd fftw-3.1.2
> > > make distclean
> > > ./configure --enable-float --enable-sse --enable-threads
> > > make
> > > make install
> > > make distclean
> > > cd ..
> > >
> > > #2.3) gromacs single
> > > tar xvfz gromacs-3.3.2.tar.gz
> > > cd gromacs-3.3.2
> > > ./configure --enable-mpi --program-suffix=_mpi
> > > --prefix=/usr/local/gromacs332
> > > make
> > > make install
> > > make links
> > > make distclean
> > > cd ..
> > >
> > > #2.4) fftw double
> > > cd fftw-3.1.2
> > > ./configure --enable-sse2 --enable-threads
> > > make
> > > make install
> > > make distclean
> > > cd ..
> > >
> > > #2.2) gromacs double
> > > cd gromacs-3.3.2
> > > ./configure --enable-mpi --program-suffix=_mpi_d
> > > --prefix=/usr/local/gromacs332 --enable-double
> > > make
> > > make install
> > > make links
> > > make distclean
> > > cd ..
> > >
> > >
> > >
> > >
> > > On Mon, Mar 3, 2008 at 3:09 PM, mario ciappy wrote:
> > > > Dear all,
> > > > I'm tried to configure gromacs in parallel but I have meet some
> > problems.
> > > > I don't understand if the problems are relative to mpi or gromacs
> > > > configuration. For this reason I'd be grateful if you explained a
> > detailed
> > > > installation procedure of all that require to run gromacs in parallel,
> > > > started by mpi/lam configuration. I now that is an hard and demanding
> > > > request, but it is a big help for me because you are only resource.
> > > >
> > > > Thank's in advance
> > > >
> > > > Mario
> > > >
> > > >
> > > > ________________________________
> > > > ________________________________
> > > >
> > > > L'email della prossima generazione? Puoi averla con la nuova Yahoo!
> Mail
> > > > _______________________________________________
> > > > gmx-users mailing list gmx-users at gromacs.org
> > > > http://www.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
> > > >
> > >
> > >
> > >
> > > --
> > > Diego Enry B. Gomes
> > > Laboratório de Modelagem e Dinamica Molecular
> > > Universidade Federal do Rio de Janeiro - Brasil.
> > > _______________________________________________
> > > gmx-users mailing list gmx-users at gromacs.org
> > > http://www.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
> > >
> > >
> > >
> > >
> > > ________________________________
> > > ________________________________
> > > L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail
> > > _______________________________________________
> > > gmx-users mailing list gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at http://www.gromacs.org/search before
> posting!
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> > > www interface or send it to gmx-users-request at gromacs.org.
> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > >
> >
> >
> >
> > --
> > Diego Enry B. Gomes
> > Laboratório de Modelagem e Dinamica Molecular
> > Universidade Federal do Rio de Janeiro - Brasil.
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.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
> >
> >
> >
> >
> > ________________________________
> > Inviato da Yahoo! Mail.
> > Il servizio di posta con lo spazio illimitato.
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
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> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
>
> --
> Diego Enry B. Gomes
> Laboratório de Modelagem e Dinamica Molecular
> Universidade Federal do Rio de Janeiro - Brasil.
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 12 Mar 2008 17:11:12 -0700 (PDT)
> From: Alan Dodd <anoddlad at yahoo.com>
> Subject: Re: [gmx-users] trjconv output at a specified time
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <638395.7541.qm at web38708.mail.mud.yahoo.com>
> Content-Type: text/plain; charset="us-ascii"
>
> Select a group: 2
> Selected 2: 'Protein-H'
> trn version: GMX_trn_file (single precision)
> Reading frame 0 time 125.000
>
> 'nuff said. Couldn't comment on the time between frames in your file.
> gmxdump will tell you, or get it from (nstxout or nstxtcout)*dt in your mdp.
>
>
>
> ----- Original Message ----
> From: Liu Shiyong <liushiyong at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Wednesday, March 12, 2008 11:24:00 PM
> Subject: Re: [gmx-users] trjconv output at a specified time
>
> Thanks.
>
> The trajectory starts at 125ps ?
>
> So step 1 == 125 ps
> step 2 == 250 ps
> step 3 == 375 ps
>
> Where is 125ps from ?
>
> But
>
> ; RUN CONTROL PARAMETERS
> integrator = steep
> ; Start time and timestep in ps
> tinit = 0
> dt = 0.002
>
>
>
>
> On Wed, Mar 12, 2008 at 5:32 PM, Alan Dodd <anoddlad at yahoo.com> wrote:
>
> You asked for the frame at 1ps. The trajectory starts at 125ps, so
> unsurprisingly the program does not give you an output.
>
>
> ----- Original Message ----
> From: Liu Shiyong <liushiyong at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Wednesday, March 12, 2008 10:07:17 PM
> Subject: [gmx-users] trjconv output at a specified time
>
> Hi,
>
> I want to output a structure in a given time, for example , in step 1 during
> minimization.
>
> I tried the following command using dump:
> trjconv -f r-l_1_oplsaa.minim_traj.trr -timestep 1 -o m.pdb -s
> r-l_1_oplsaa.input.tpr -t0 0 -dump 1
>
> But It didnot work.
>
> Output msg:
>
> Select a group: 2
> Selected 2: 'Protein-H'
> trn version: GMX_trn_file (single precision)
> Reading frame 0 time 125.000
> Back Off! I just backed up m.pdb to ./#m.pdb.1#
> Last frame 19 time 2418.000
>
> WARNING no output, trajectory ended at 2418
>
>
> gcq#76: "Baseball Heroes Only" (P.J. Harvey)
>
> Best
>
> --
> Shiyong Liu
> Research Assistant
> center for bioinformatics in the university of kansas
> Lab: (785)864-1962
> Email: syliu at ku.edu (shiyongliu at ku.edu or liushiyong at ku.edu)
> Homepage: http://www.people.ku.edu/~syliu
> Lab: http://vakser.bioinformatics.ku.edu/people
> Phone: (785) 864-1962
>
>
> -----Inline Attachment Follows-----
>
> _______________________________________________
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> http://www.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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> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
>
> --
> Shiyong Liu
> Research Assistant
> center for bioinformatics in the university of kansas
> Lab: (785)864-1962
> Email: syliu at ku.edu (shiyongliu at ku.edu or liushiyong at ku.edu)
> Homepage: http://www.people.ku.edu/~syliu
> Lab: http://vakser.bioinformatics.ku.edu/people
> Phone: (785) 864-1962
>
>
> -----Inline Attachment Follows-----
>
> _______________________________________________
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> http://www.gromacs.org/mailman/listinfo/gmx-users
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> 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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>
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
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