Quoting "Rigden, LucianeVMello" <[EMAIL PROTECTED]>: > 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----- > From: [EMAIL PROTECTED] on behalf of > [EMAIL PROTECTED] > Sent: Thu 3/13/2008 12:12 AM > To: [email protected] > Subject: gmx-users Digest, Vol 47, Issue 39 > > Send gmx-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > [EMAIL PROTECTED] > > You can reach the person managing the list at > [EMAIL PROTECTED] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > 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" <[email protected]> > 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 <[email protected]> > > 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----- > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > 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 > > > > > > __________________________________________________ > > Do You Yahoo!? > > Tired of spam? Yahoo! Mail has the best spam protection around > > http://mail.yahoo.com > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > 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 > > > > > > -- > 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20080312/c9115ee7/attachment-0001.html > > ------------------------------ > > 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" <[email protected]> > 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 [email protected] > > > > 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 [email protected] > > > 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 [email protected] > > > 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 [email protected] > > 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 > > > > > > > > > > ________________________________ > > Inviato da Yahoo! Mail. > > Il servizio di posta con lo spazio illimitato. > > _______________________________________________ > > gmx-users mailing list [email protected] > > 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. > > > ------------------------------ > > 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 <[email protected]> > 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 <[email protected]> > 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 <[email protected]> > 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 > > > -----Inline Attachment Follows----- > > _______________________________________________ > gmx-users mailing list [email protected] > 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 > > > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > > _______________________________________________ > gmx-users mailing list [email protected] > 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 > > > > > -- > 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 > > > -----Inline Attachment Follows----- > > _______________________________________________ > gmx-users mailing list [email protected] > 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 > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20080312/8a8bf49f/attachment.html > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 47, Issue 39 > ***************************************** > > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] 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
