[gmx-users] gromacs synaptic package manager

[Roland Schulz]

As Justin said: Look at one of the many tutorials.

Roland

2010/10/1 ahmet yıldırım <ahmedo047 at gmail.com>

> Dear Roland,
>
> Eventually I installed the installation steps with
> "./configure --prefix=$HOME/usr "as you said. can you send me the input
> file for test?
> I want to run a simulation. how can I do this?
>
> Thanks for your helps
>
>
> 2010/10/2 Roland Schulz <roland at utk.edu>
>
>>  Hi,
>>
>> either install as root by running:
>> sudo make install
>>
>> or rerun the installation steps with
>> ./configure --prefix=$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
>>>>
>>>> ========================================
>>>> --
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>>>
>>>
>>>
>>> --
>>> Ahmet YILDIRIM
>>>
>>> --
>>>
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>>
>>
>>
>> --
>> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
>> 865-241-1537, ORNL PO BOX 2008 MS6309
>>
>> --
>>
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>
>
>
> --
> Ahmet YILDIRIM
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
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-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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