[gmx-users] Gromacs installation question: Where is my Gromacs?

[Justin A. Lemkul]

bestenborstel wrote:
> Did run sudo make install again, but before I executed configure with prefix=/usr/local/gromacs and I did mkdir gromacs in /usr/local before manually. Content in the gromacs folder: bin	include	lib	share
> 
> Gromacs finished again with:
> 
> GROMACS is installed under /usr/local/gromacs.
> Make sure to update your PATH and MANPATH to find the
> programs and unix manual pages, and possibly LD_LIBRARY_PATH
> or /etc/ld.so.conf if you are using dynamic libraries.
> 
> Please run "make tests" now to verify your installation.
> 
> If you want links to the executables in /usr/local/bin,
> you can issue "make links" now.
> 
> 
> Shall I execute now 'sudo make links' or 'make links', please? Sorry, I also don't really know how to update my PATH variable. 

You need sudo.  It will write links into /usr/local/bin.  It is not strictly 
necessary, as you can follow:

http://www.gromacs.org/Documentation/Installation_Instructions#Getting_access_to_GROMACS_after_installation

The GMXRC script magically configures your environment for you.

> Do I have to execute 'make test' as the Gromacs page says test set is broken?

No, it won't do anything.

> Finally, is there something like 'make clean'  to allow for a proper, clean re-installation?
> 

Yes.

-Justin

> I thought I better ask again.
> Sorry.
> Gudrun
> 
> 
> Am 16.03.2012 um 20:05 schrieb David van der Spoel:
> 
>> On 2012-03-16 21:03, bestenborstel wrote:
>>> Sorry, David, not sure what you mean. Yes, I am the admin of my pc. I can do whatever I can :-)
>>> What do you ask me please to do?
>> sudo make install
>> and check on the screen where the stuff is copied to.
>>
>>> Am 16.03.2012 um 19:54 schrieb David van der Spoel:
>>>
>>>> On 2012-03-16 20:49, bestenborstel wrote:
>>>>> Thank you for your quick reply.
>>>>>
>>>>> 'make links' produces:
>>>>>
>>>>> Saturn:gromacs-4.5.5 gudrun$ make links
>>>>> cd /usr/local/gromacs/bin&&   programs=`ls`&&   cd /usr/local/bin&&   \
>>>>> 	for i in $programs; do \
>>>>> 	   (test ! -f $i&&   ln -s /usr/local/gromacs/bin/$i . ; exit 0); \
>>>>> 	done
>>>>> /bin/sh: line 0: cd: /usr/local/gromacs/bin: No such file or directory
>>>>> make: *** [links] Error 1
>>>>>
>>>>> I have a /usr/local/ but there is no gromacs. Not even after running again 'sudo make -n install'
>>>>> Sorry, I am not sure where to post this lengthy output.
>>>>>
>>>> -n means "not really"
>>>> run it without to install.
>>>> But do you have permission to write in /usr/local?
>>>>
>>>>> Thank you for your help.
>>>>> Kind regards
>>>>> Gudrun
>>>>>
>>>>
>>>> --
>>>> David van der Spoel, Ph.D., Professor of Biology
>>>> Dept. of Cell&  Molec. Biol., Uppsala University.
>>>> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
>>>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>>>> --
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>>
>> -- 
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>> -- 
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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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