[gmx-users] Gromacs Installation

Justin A. Lemkul jalemkul at vt.edu
Tue Feb 15 03:46:47 CET 2011

majid hasan wrote:
> Okay, I'll try with --enable-single. But as far as I understood, it 
> seems like its an issue with --enable-shared. In the first attempt, I 
> did enable-shared in fftw configuration, but didn't do it in gromacs 
> configuration, and got this error. In the second attempt, I did 
> enable-shared in ./configure for both fftw and gromacs, but still got 
> the same message. In the third attempt, I didn't enable shared anywhere, 
> and installation went well. Only issue is that when I run ngmx, it says 
> "command not found", and I can't view .trr file, but this seems to be a 
> different issue. But I don't know why --enable-shared isn't working.
> About installing in home directory: actually I downloaded the source 
> from gromacs website, and I did manage to install it in my home 
> directory. But some of the commands, like luck, and ngmx are missing. 
> When I type any of luck, I get, command not found and you can install it 
> by typing sudo apt-get install gromacs. I did try to download it using 
> apt-get and software center in ubuntu, but it installs it in 
> usr/share/gromacs, but I want to install it in my home directory.

In the latest version of Gromacs, "luck" is named "g_luck."  If ngmx was not 
installed, then probably the required X11 libraries were not found on your 
system.  Check the output from configuration (i.e. config.log) for details.


> Thanks,
> Majid
> ------------------------------------------------------------------------
> *From:* lina zhao <lnzhao99 at gmail.com>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Mon, February 14, 2011 6:24:47 PM
> *Subject:* Re: [gmx-users] Gromacs Installation
> 1. Seems the default fftw configuration is double,
>     when you install the fftw-3.2.2 configure with --enable single.
> 2. about your question:"I wanted to ask if I can download gromacs in my 
> home directory using the ubuntu software center or synaptic manager?"
> 1] You can download in your home directory and install.
> 2] a better but a bit not so-easy way, is download the source 
> (http://packages.debian.org/sid/gromacs), built the package and add it 
> into repository.
> There maybe also some other ways.
> HTH,
> lina
> On Tue, Feb 15, 2011 at 6:23 AM, majid hasan <pu_majidhasan at yahoo.com 
> <mailto:pu_majidhasan at yahoo.com>> wrote:
>     Dear All,
>     I am trying to install gromacs in ubuntu. I configured both fftw and
>     gromacs in my home folder following the instructions on
>     http://www.gromacs.org/Downloads/Installation_Instructions. However,
>     when I  do "make", I get an error in the end (pasted below). I have
>     also attached the log file of compilation with the email.
>     /usr/bin/ld: /home/majid/user/soft/fftw/lib/libfftw3f.a(mapflags.o):
>     relocation R_X86_64_32 against `.rodata' can not be used when making
>     a shared object; recompile with -fPIC
>     /home/majid/user/soft/fftw/lib/libfftw3f.a: could not read symbols:
>     Bad value
>     collect2: ld returned 1 exit status
>     make[3]: *** [libmd.la <http://libmd.la>] Error 1
>     make[3]: Leaving directory `/home/majid/user/down/gromacs/src/mdlib'
>     make[2]: *** [all-recursive] Error 1
>     make[2]: Leaving directory `/home/majid/user/down/gromacs/src'
>     make[1]: *** [all] Error 2
>     make[1]: Leaving directory `/home/majid/user/down/gromacs/src'
>     make: *** [all-recursive] Error 1
>     Moreover, I wanted to ask if I can download gromacs in my home
>     directory using the ubuntu software center or synaptic manager?
>     Thanks,
>     Majid
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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