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
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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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" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] trjconv output at a specified time
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Message-ID:
<[EMAIL PROTECTED]>
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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]>
> To: Discussion list for GROMACS users <gmx-users@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: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED])
> 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-----
>
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--
Shiyong Liu
Research Assistant
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED])
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" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] problem with mpi configuration.
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Message-ID:
<[EMAIL PROTECTED]>
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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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@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 [EMAIL PROTECTED]
> > > 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@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 [EMAIL PROTECTED]
> > 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@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 [EMAIL PROTECTED]
> > 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@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 [EMAIL PROTECTED]
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>
>
>
>
> ________________________________
> Inviato da Yahoo! Mail.
> Il servizio di posta con lo spazio illimitato.
> _______________________________________________
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--
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 <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] trjconv output at a specified time
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
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 <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users <gmx-users@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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users <gmx-users@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: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED])
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
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--
Shiyong Liu
Research Assistant
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED])
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
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