http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions#Getting_access_to_GROMACS_after_installation
-Justin
ahmet yıldırım wrote:
Hi,
When I run the pdb2gmx, it is giving the error as folllowing. What can I do?
Thanks in advance
a...@ab-desktop:~/Masaüstü/gromacs-4.5.1/src/kernel$ pdb2gmx -h
The program 'pdb2gmx' is currently not installed. You can install it by
typing:
sudo apt-get install gromacs
bash: pdb2gmx: command not found
-h
The program 'pdb2gmx' is currently not installed. You can install it by
typing:
sudo apt-get install gromacs
bash: pdb2gmx: command not found
02 Ekim 2010 02:08 tarihinde Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> yazdı:
ahmet yıldırım wrote:
Dear Roland,
Eventually I installed the installation steps with "./configure
--prefix=$HOME/usr "as you said. can you send me the input file
for test?
I want to run a simulation. how can I do this?
Please do some tutorial material. I sent you the link before.
-Justin
Thanks for your helps
2010/10/2 Roland Schulz <rol...@utk.edu <mailto:rol...@utk.edu>
<mailto:rol...@utk.edu <mailto:rol...@utk.edu>>>
Hi,
either install as root by running:
sudo make install
or rerun the installation steps with ./configure
--prefix=$HOME/usr
to install it in your home directory.
Roland
2010/10/1 ahmet yıldırım <ahmedo...@gmail.com
<mailto:ahmedo...@gmail.com>
<mailto:ahmedo...@gmail.com <mailto:ahmedo...@gmail.com>>>
Dear justin,
Thanks for your reply. I did that you said. I tried to
install
Gromacs 4.5.1but I failed it. I enter this line "
a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 make install " in
terminal. What can I do? I am sorry. I am a new user.
Thanks in advance
1. I installed fftw 3.2.2
a...@ab-desktop:~/Masaüstü/ cd fftw-3.2.2
a...@ab-desktop:~/Masaüstü/fftw-3.2.2
a...@ab-desktop:~/Masaüstü/fftw-3.2.2 ./configure
--enable-threads --enable-float
a...@ab-desktop:~/Masaüstü/fftw-3.2.2 make
a...@ab-desktop:~/Masaüstü/fftw-3.2.2 make install
2. I tried to install Gromacs 4.5.1
a...@ab-desktop:~/Masaüstü/ cd gromacs-4.5.1
a...@ab-desktop:~/Masaüstü/gromacs-4.5.1
a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 ./configure
a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 make
a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 make install
Making install in include
make[1]: Entering directory
`/home/ab/Masaüstü/gromacs-4.5.1/include'
Making install in .
make[2]: Entering directory
`/home/ab/Masaüstü/gromacs-4.5.1/include'
make[3]: Entering directory
`/home/ab/Masaüstü/gromacs-4.5.1/include'
make[3]: Nothing to be done for `install-exec-am'.
test -z "/usr/local/gromacs/include/gromacs" || /bin/mkdir -p
"/usr/local/gromacs/include/gromacs"
/bin/mkdir: cannot create directory `/usr/local/gromacs':
Permission denied
make[3]: *** [install-pkgincludeHEADERS] Error 1
make[3]: Leaving directory
`/home/ab/Masaüstü/gromacs-4.5.1/include'
make[2]: *** [install-am] Error 2
make[2]: Leaving directory
`/home/ab/Masaüstü/gromacs-4.5.1/include'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory
`/home/ab/Masaüstü/gromacs-4.5.1/include'
make: *** [install-recursive] Error 1
2010/10/1 Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>
ahmet yıldırım wrote:
Hi,
I've installed GROMACS 4.0.3 and MPI libraries using
Ubuntu 9.04 Synaptic Package Manager. What else
should I do?
I want to run a simulation in parallel on a
single PC.
Which commands should I enter the terminal?
If I were you, I would uninstall this version (which is
outdated by nearly 2 years!) and get version 4.5.1.
Installing from source is quite easy. Not only will you
benefit from hundreds of bug fixes and enhancements, but
running in parallel on a multi-core machine is no longer
MPI-dependent, making it somewhat easier.
For usage and instructions, see the manual and any of the
numerous tutorials linked here:
http://www.gromacs.org/Documentation/Tutorials#General
-Justin
Thanks a lot for any instruction.
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> |
(540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
Ahmet YILDIRIM
--
========================================
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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