As Justin said: Look at one of the many tutorials. Roland
2010/10/1 ahmet yıldırım <ahmedo...@gmail.com> > Dear Roland, > > Eventually I installed the installation steps with > "./configure --prefix=$HOME/usr "as you said. can you send me the input > file for test? > I want to run a simulation. how can I do this? > > Thanks for your helps > > > 2010/10/2 Roland Schulz <rol...@utk.edu> > >> Hi, >> >> either install as root by running: >> sudo make install >> >> or rerun the installation steps with >> ./configure --prefix=$HOME/usr >> to install it in your home directory. >> >> Roland >> >> 2010/10/1 ahmet yıldırım <ahmedo...@gmail.com> >> >>> Dear justin, >>> >>> Thanks for your reply. I did that you said. I tried to install Gromacs >>> 4.5.1but I failed it. I enter this line " >>> a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 >>> make install " in terminal. What can I do? I am sorry. I am a new user. >>> >>> Thanks in advance >>> >>> 1. I installed fftw 3.2.2 >>> a...@ab-desktop:~/Masaüstü/ cd fftw-3.2.2 >>> a...@ab-desktop:~/Masaüstü/fftw-3.2.2 >>> a...@ab-desktop:~/Masaüstü/fftw-3.2.2 ./configure --enable-threads >>> --enable-float >>> a...@ab-desktop:~/Masaüstü/fftw-3.2.2 make >>> a...@ab-desktop:~/Masaüstü/fftw-3.2.2 make install >>> >>> 2. I tried to install Gromacs 4.5.1 >>> a...@ab-desktop:~/Masaüstü/ cd gromacs-4.5.1 >>> a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 >>> a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 ./configure >>> a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 make >>> a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 make install >>> Making install in include >>> make[1]: Entering directory `/home/ab/Masaüstü/gromacs-4.5.1/include' >>> Making install in . >>> make[2]: Entering directory `/home/ab/Masaüstü/gromacs-4.5.1/include' >>> make[3]: Entering directory `/home/ab/Masaüstü/gromacs-4.5.1/include' >>> make[3]: Nothing to be done for `install-exec-am'. >>> test -z "/usr/local/gromacs/include/gromacs" || /bin/mkdir -p >>> "/usr/local/gromacs/include/gromacs" >>> /bin/mkdir: cannot create directory `/usr/local/gromacs': Permission >>> denied >>> make[3]: *** [install-pkgincludeHEADERS] Error 1 >>> make[3]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include' >>> make[2]: *** [install-am] Error 2 >>> make[2]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include' >>> make[1]: *** [install-recursive] Error 1 >>> make[1]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include' >>> make: *** [install-recursive] Error 1 >>> >>> >>> >>> 2010/10/1 Justin A. Lemkul <jalem...@vt.edu> >>> >>> >>>> >>>> ahmet yıldırım wrote: >>>> >>>>> Hi, >>>>> >>>>> I've installed GROMACS 4.0.3 and MPI libraries using Ubuntu 9.04 >>>>> Synaptic Package Manager. What else should I do? >>>>> I want to run a simulation in parallel on a single PC. Which commands >>>>> should I enter the terminal? >>>>> >>>>> >>>> If I were you, I would uninstall this version (which is outdated by >>>> nearly 2 years!) and get version 4.5.1. Installing from source is quite >>>> easy. Not only will you benefit from hundreds of bug fixes and >>>> enhancements, but running in parallel on a multi-core machine is no longer >>>> MPI-dependent, making it somewhat easier. >>>> >>>> For usage and instructions, see the manual and any of the numerous >>>> tutorials linked here: >>>> >>>> http://www.gromacs.org/Documentation/Tutorials#General >>>> >>>> -Justin >>>> >>>> >>>> Thanks a lot for any instruction. >>>>> >>>>> >>>>> >>>> -- >>>> ======================================== >>>> >>>> Justin A. Lemkul >>>> Ph.D. Candidate >>>> ICTAS Doctoral Scholar >>>> MILES-IGERT Trainee >>>> Department of Biochemistry >>>> Virginia Tech >>>> Blacksburg, VA >>>> jalemkul[at]vt.edu | (540) 231-9080 >>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>>> >>>> ======================================== >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>>> Please don't post (un)subscribe requests to the list. Use the www >>>> interface or send it to gmx-users-requ...@gromacs.org. >>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>> >>> >>> >>> -- >>> Ahmet YILDIRIM >>> >>> -- >>> >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> >> >> -- >> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov >> 865-241-1537, ORNL PO BOX 2008 MS6309 >> >> -- >> >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > Ahmet YILDIRIM > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309
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