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

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 16 21:51:24 CET 2012



bestenborstel wrote:
> Again 'sudo make links'  gives:
> 
> 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
> 
> Is this good or bad, please?
> 

In the absence of an error message, nothing is wrong.

> g_luck is located for example now in /usr/local/bin/g_luck when I do 'which g_luck'
> Would you recommend to re-install, although it seems to work now? 

I see no need for a reinstall.  It appears to be working as expected.

-Justin

> Thank you for your help.
> 
> Thank you.
> Kind regards
> Gudrun
> 
> 
> Am 16.03.2012 um 20:28 schrieb 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
>>>>>> --
>>>>>> 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
>>>> -- 
>>>> 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
>>>> -- 
>>>> 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
>> -- 
>> ========================================
>>
>> 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
> 

-- 
========================================

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

========================================



More information about the gromacs.org_gmx-users mailing list