[gmx-users] Installing & uninstalling of gromacs

Spring buds winterhot82 at gmail.com
Sat Jan 28 14:03:42 CET 2012 

On Wed, Jan 25, 2012 at 7:42 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  On 25/01/2012 12:54 AM, Spring buds wrote:
>
>
>  Removing files in /usr/local/gromacs has no bearing on the contents of
>> /usr/local/bin.  If you did 'make links' at the end of the installation,
>> you will have dead links in /usr/local/bin that need to be removed, as well.
>>
>> -Justin
>>
>
>
> Dear Justin,
>
> Thanks a lot for your insight.
>
> I did links in the end so there is links in  */usr/local/bin*. After
> uninstall I still have dead links with */usr/local/bin. *could you help
> me how to remove this* *in* **/usr/local/bin*.
>
>
> 1. cd /usr/local/bin
> 2. ls -l
> 3. look for broken links
> 4. sudo rm <names of broken links>
>
> Hint: the majority of them will be named g_xxx so that makes for easy
> wildcarding.
>
> Mark
>
>
> Dear Mark,

Your reply was very helpful. Thanks.



>
>
>
>
>
>
>>
>>
>>>
>>>    try make uninstall in the directory where you used make install
>>>    before. like Path_to//gromacs-4.5.5
>>>    and then make distclean
>>>    for a totally clear re-installation, removed the /gromac-4.5.5 and
>>>
>>>    re-untar the gromacs-4.5.5.tar.gz
>>>
>>>    before that, further check the lib and bin have totally removed or
>>> not.
>>>
>>>
>>> Sure. I will do now
>>>
>>>
>>>    Which OS you are working on?
>>>
>>>
>>> Linux (CentOS 5.7)
>>>
>>> Thanks a lot.
>>>
>>>
>>>     >
>>>     >
>>>     > On Tue, Jan 24, 2012 at 2:31 AM, lina <lina.lastname at gmail.com
>>>     <mailto:lina.lastname at gmail.com>> wrote:
>>>     >>
>>>     >> On 24 Jan, 2012, at 1:53, Spring buds <winterhot82 at gmail.com
>>>      <mailto:winterhot82 at gmail.com>> wrote:
>>>     >>
>>>     >> > Dear Gromacs users,
>>>     >> >
>>>     >> > Greetings!!!
>>>     >> >
>>>     >> > I am very new users and I am trying to install grmacs 4.5.5 or
>>>    3.3.3 for
>>>     >> > past four days. But still I am not able to. So I would like to
>>>    ask some
>>>     >> > questions which are below.
>>>     >> >
>>>     >> >
>>>     >> > 1.My laptop is a dual core, which means two processors?.So
>>>    should I need
>>>     >> > to install MPI?
>>>     >> >
>>>     >> --enable threads
>>>     >>
>>>     >> > 2.I installed gromacs 4.5.5 with mistakes. To remove
>>>    installing, I used
>>>     >> > the "which gromacs" and it shows as "/usr/bin/which: no mdrun in
>>>     >> >
>>>
>>>  (/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/home/Malai/bin)".
>>>     >> > However, I used "rm -rf /usr/local/gromacs" to remove
>>>    installing I still can
>>>     >> > see tha gromacs files with red background in "/usr/local/bin".
>>>    Could you
>>>     >> > tell me I removed the gromacs installing?
>>>     >>
>>>     >> You have not.
>>>     >>
>>>     >> >
>>>     >> > 3.Could you please tell me the very simple steps for
>>>    installatios, since
>>>     >> > I am a novice.
>>>     >>
>>>     >> http://www.gromacs.org/Downloads/Installation_Instructions
>>>     >>
>>>     >> >
>>>     >> > Many thanks in advance for your time and help.
>>>     >> >
>>>     >> > Huang Malai
>>>     >> > --
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>> --
>> ========================================
>>
>> 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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>
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