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