[gmx-users] gromacs synaptic package manager

[ahmet yıldırım]

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 <roland at 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 <ahmedo047 at 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 " 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
>>
>> --
>>
>> 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
>>
>
>
>
> --
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
> 865-241-1537, ORNL PO BOX 2008 MS6309
>
> --
> 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/fd03ed9c/attachment.html>