Thank you Mr.David. On Thu, Mar 13, 2008 at 6:45 PM, <[EMAIL PROTECTED]> wrote:
> Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > 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. Problem about *pdbgmx (sudheer babu) > 2. Re: Problem about *pdbgmx (David van der Spoel) > 3. Re: problem with mpi configuration. (Dr. Niharendu Choudhury) > 4. Re: problem with mpi configuration. (Mark Abraham) > 5. downloading problem (Siavoush Dastmalchi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 13 Mar 2008 16:39:25 +0530 > From: "sudheer babu" <[EMAIL PROTECTED]> > Subject: [gmx-users] Problem about *pdbgmx > To: gmx-users@gromacs.org > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="iso-8859-1" > > Hi gmx-users, > I want to protonate only HIS residues in my protein , so I gave command > like this *pdb2gmx -f protein.pdb -HIS then it asked which number of HIS > to > protonate, I gave numbers of HIS residues which I want protonate , it ran > fine without error, but when I open conf.gro file, along with HISH, LYS > also > protonating and form LYSH. In input file LYS present like this. Why it > happening like this? > Pls help me. > Thanks in advance. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20080313/9258929c/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Thu, 13 Mar 2008 12:12:17 +0100 > From: David van der Spoel <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Problem about *pdbgmx > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > sudheer babu wrote: > > Hi gmx-users, > > I want to protonate only HIS residues in my protein , so I gave > > command like this *pdb2gmx -f protein.pdb -HIS then it asked which > > number of HIS to protonate, I gave numbers of HIS residues which I want > > protonate , it ran fine without error, but when I open conf.gro file, > > along with HISH, LYS also protonating and form LYSH. In input file LYS > > present like this. Why it happening like this? > > that's default. use -lys flag and -arg and -glu and -asp > > > Pls help me. > > Thanks in advance. > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 > > > -- > David van der Spoel, Ph.D. > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > > > ------------------------------ > > Message: 3 > Date: Thu, 13 Mar 2008 16:57:45 +0530 (IST) > From: "Dr. Niharendu Choudhury" <[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 > > Dear Pohl, > I think your prefix directory /usr/local/gromacs332 is not accesible for > writting. Try to creat new directories with other names and use those in > prefix. > > Have you setenv for the include and lib of the fftw files? > > (For instance, assume we have installed FFTW with --prefix=/home/joe/fftw. > If your shell is tcsh, you set > > setenv CPPFLAGS -I/home/joe/fftw/include > setenv LDFLAGS -L/home/joe/fftw/lib > > or, if you are using a bash shell: > > export CPPFLAGS=-I/home/joe/fftw/include > export LDFLAGS=-L/home/joe/fftw/lib ) > > If not do that. > > Nihar > > > > > > > Quoting Jens Pohl <[EMAIL PROTECTED]>: > > > > > > -----Ursprüngliche Nachricht----- > > > Von: Discussion list for GROMACS users <gmx-users@gromacs.org> > > > Gesendet: 12.03.08 20:06:55 > > > An: Discussion list for GROMACS users <gmx-users@gromacs.org> > > > Betreff: Re: [gmx-users] problem with mpi configuration. > > > > > > > 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. > > > > Hallo Mario! > > (Maybe) you have to install as root. When I tried to install gromacs as > user, > > I had similar problems. > > Jens > > > > > > > > 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<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! > > > > 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 > > > > > > > > > > > > > > > > > > ----------------------------------------------------------------- > > > Inviato da Yahoo! Mail. > > > > > > Il servizio di posta con lo spazio illimitato. > > > > > > ----------------------------------------------------------------- > > > _______________________________________________ > > > 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 > > > > > > > > > _______________________________________________________________________ > > Jetzt neu! Schützen Sie Ihren PC mit McAfee und WEB.DE. 30 Tage > > kostenlos testen. http://www.pc-sicherheit.web.de/startseite/?mc=022220 > > > > _______________________________________________ > > 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 > > > > > > ************************************************************************* > * * > * Dr. Niharendu Choudhury Tel: 91-22-2559 5089 * > * Theoretical Chemistry Section, Fax: 91-22-2550 5151 * > * RC & CD Division, Chemistry Group, 91-22-2551-9613 * > * Mod. Lab, Email: [EMAIL PROTECTED] * > * Trombay, Mumbai-400 085 * > * INDIA * > * * > * Residence Tel. No. 91-22-2552 7832 * > ************************************************************************* > > > ------------------------------------------------- > > > > ------------------------------ > > Message: 4 > Date: Thu, 13 Mar 2008 23:51:47 +1100 > From: Mark Abraham <[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; format=flowed > > Dr. Niharendu Choudhury wrote: > > Dear Pohl, > > I think your prefix directory /usr/local/gromacs332 is not accesible for > > writting. Try to creat new directories with other names and use those in > > prefix. > > First, they need to fix their typo in their configure command line, as > mentioned by another poster. Otherwise, it isn't known that the failure > to write these files is caused by permission issues, rather than their > malformed filename. > > > Have you setenv for the include and lib of the fftw files? > > > > (For instance, assume we have installed FFTW with > --prefix=/home/joe/fftw. > > If your shell is tcsh, you set > > > > setenv CPPFLAGS -I/home/joe/fftw/include > > setenv LDFLAGS -L/home/joe/fftw/lib > > > > or, if you are using a bash shell: > > > > export CPPFLAGS=-I/home/joe/fftw/include > > export LDFLAGS=-L/home/joe/fftw/lib ) > > > > If not do that. > > This works, but it's superior to leave the environment alone and instead > to use "./configure CPPFLAGS=-I/home/joe/fftw/include > LDFLAGS=-L/home/joe/fftw/lib". Not only do you avoid having to get it > right for each shell, but you don't pollute your environment for this > shell (small point), and (more importantly) in config.log you will have > a record of the command line for any subsequent time you need to run > configure. When someone has to come back in 6 months to configure an MPI > or double-precision version, the record of what was done last time saves > on repeated detective work. > > If you need multiple -I or -L flags, then enclosing them in quotes, > separated by spaces, works, i.e. "./configure LDFLAGS='-L/some/lib > -L/some/other/lib'" > > Mark > > > ------------------------------ > > Message: 5 > Date: Thu, 13 Mar 2008 16:44:14 +0330 > From: "Siavoush Dastmalchi" <[EMAIL PROTECTED]> > Subject: [gmx-users] downloading problem > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="windows-1256" > > Hi there, > > This may not be relevant to this list but I am hopping to get an answer. > The problem is that I can't download the source code for Grommacs from the > download site and it seems that the link to web interface to the ftp server > is not working as well. > > I tried to use an ftp program to connect to ftp.gromacs.org but wasn't > sure what should I use for User Name and Password. > > Many thanks in advance. > > Siavoush > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: not available > Type: application/ms-tnef > Size: 3100 bytes > Desc: not available > Url : > http://www.gromacs.org/pipermail/gmx-users/attachments/20080313/3b7e67b8/attachment.bin > > ------------------------------ > > _______________________________________________ > 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! > > End of gmx-users Digest, Vol 47, Issue 41 > ***************************************** >
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