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

[bestenborstel]

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?

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? 
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