[gmx-users] gromacs synaptic package manager

[ahmet yıldırım]

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 "
ab at 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
ab at ab-desktop:~/Masaüstü/ cd fftw-3.2.2
ab at ab-desktop:~/Masaüstü/fftw-3.2.2
ab at ab-desktop:~/Masaüstü/fftw-3.2.2  ./configure --enable-threads
--enable-float
ab at ab-desktop:~/Masaüstü/fftw-3.2.2 make
ab at ab-desktop:~/Masaüstü/fftw-3.2.2 make install

2. I tried to install Gromacs 4.5.1
ab at ab-desktop:~/Masaüstü/ cd gromacs-4.5.1
ab at ab-desktop:~/Masaüstü/gromacs-4.5.1
ab at ab-desktop:~/Masaüstü/gromacs-4.5.1 ./configure
ab at ab-desktop:~/Masaüstü/gromacs-4.5.1 make
ab at 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 <jalemkul at 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 If I were you, I would uninstall this version (which is outdated by nearly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 at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Ahmet YILDIRIM
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101002/ba4df899/attachment.html>