As Justin said: Look at one of the many tutorials.<div><br></div><div>Roland<br><div><br><div class="gmail_quote">2010/10/1 ahmet yıldırım <span dir="ltr"><<a href="mailto:ahmedo047@gmail.com">ahmedo047@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Dear Roland,<br><br>Eventually I installed the installation steps with <div>"./configure --prefix=$HOME/usr "as you said. can you send me the input file for test?<br>
I want to run a simulation. how can I do this?<br>
<br>Thanks for your helps<br></div><br><br><div class="gmail_quote">2010/10/2 Roland Schulz <span dir="ltr"><<a href="mailto:roland@utk.edu" target="_blank">roland@utk.edu</a>></span><br><blockquote class="gmail_quote" style="border-left:1px solid rgb(204, 204, 204);margin:0pt 0pt 0pt 0.8ex;padding-left:1ex">
<div><div></div><div class="h5">
Hi,<div><br></div><div>either install as root by running:</div><div>sudo make install</div><div><br></div><div>or rerun the installation steps with </div><div>./configure --prefix=$HOME/usr</div><div>to install it in your home directory.</div>
<div><br></div><div>Roland</div><div><br><div class="gmail_quote">2010/10/1 ahmet yıldırım <span dir="ltr"><<a href="mailto:ahmedo047@gmail.com" target="_blank">ahmedo047@gmail.com</a>></span><br><blockquote class="gmail_quote" style="border-left:1px solid rgb(204, 204, 204);margin:0pt 0pt 0pt 0.8ex;padding-left:1ex">
<div><div></div><div>
Dear justin,<br><br>Thanks for your reply. I did that you said. I tried to install Gromacs 4.5.1but I failed it. I enter this line " ab@ab-desktop:~/Masaüstü/gromacs-4.5.1 make install " in terminal. What can I do? I am sorry. I am a new user.<br>
<br>Thanks in advance<br><br><span style="color:rgb(102, 0, 0)">1. I installed fftw 3.2.2</span><br>ab@ab-desktop:~/Masaüstü/ cd fftw-3.2.2<br>ab@ab-desktop:~/Masaüstü/fftw-3.2.2<br>ab@ab-desktop:~/Masaüstü/fftw-3.2.2 ./configure --enable-threads --enable-float<br>
ab@ab-desktop:~/Masaüstü/fftw-3.2.2 make<br>ab@ab-desktop:~/Masaüstü/fftw-3.2.2 make install<br><br style="color:rgb(102, 0, 0)"><span style="color:rgb(102, 0, 0)">2. I tried to install Gromacs 4.5.1</span><br>ab@ab-desktop:~/Masaüstü/ cd gromacs-4.5.1<br>
ab@ab-desktop:~/Masaüstü/gromacs-4.5.1<br>ab@ab-desktop:~/Masaüstü/gromacs-4.5.1 ./configure<br>ab@ab-desktop:~/Masaüstü/gromacs-4.5.1 make<br>ab@ab-desktop:~/Masaüstü/gromacs-4.5.1 make install<br><span style="color:rgb(255, 0, 0)">Making install in include</span><br style="color:rgb(255, 0, 0)">
<span style="color:rgb(255, 0, 0)">make[1]: Entering directory `/home/ab/Masaüstü/gromacs-4.5.1/include'</span><br style="color:rgb(255, 0, 0)"><span style="color:rgb(255, 0, 0)">Making install in .</span><br style="color:rgb(255, 0, 0)">
<span style="color:rgb(255, 0, 0)">make[2]: Entering directory `/home/ab/Masaüstü/gromacs-4.5.1/include'</span><br style="color:rgb(255, 0, 0)"><span style="color:rgb(255, 0, 0)">make[3]: Entering directory `/home/ab/Masaüstü/gromacs-4.5.1/include'</span><br style="color:rgb(255, 0, 0)">
<span style="color:rgb(255, 0, 0)">make[3]: Nothing to be done for `install-exec-am'.</span><br style="color:rgb(255, 0, 0)"><span style="color:rgb(255, 0, 0)">test -z "/usr/local/gromacs/include/gromacs" || /bin/mkdir -p "/usr/local/gromacs/include/gromacs"</span><br style="color:rgb(255, 0, 0)">
<span style="color:rgb(255, 0, 0)">/bin/mkdir: cannot create directory `/usr/local/gromacs': Permission denied</span><br style="color:rgb(255, 0, 0)"><span style="color:rgb(255, 0, 0)">make[3]: *** [install-pkgincludeHEADERS] Error 1</span><br style="color:rgb(255, 0, 0)">
<span style="color:rgb(255, 0, 0)">make[3]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include'</span><br style="color:rgb(255, 0, 0)"><span style="color:rgb(255, 0, 0)">make[2]: *** [install-am] Error 2</span><br style="color:rgb(255, 0, 0)">
<span style="color:rgb(255, 0, 0)">make[2]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include'</span><br style="color:rgb(255, 0, 0)"><span style="color:rgb(255, 0, 0)">make[1]: *** [install-recursive] Error 1</span><br style="color:rgb(255, 0, 0)">
<span style="color:rgb(255, 0, 0)">make[1]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include'</span><br style="color:rgb(255, 0, 0)"><span style="color:rgb(255, 0, 0)">make: *** [install-recursive] Error 1</span><br style="color:rgb(255, 0, 0)">
<br>
<br><br><div class="gmail_quote">2010/10/1 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span><div><div></div><div><br><blockquote class="gmail_quote" style="border-left:1px solid rgb(204, 204, 204);margin:0pt 0pt 0pt 0.8ex;padding-left:1ex">
<div><br>
<br>
ahmet yıldırım wrote:<br>
<blockquote class="gmail_quote" style="border-left:1px solid rgb(204, 204, 204);margin:0pt 0pt 0pt 0.8ex;padding-left:1ex">
Hi,<br>
<br>
I've installed GROMACS 4.0.3 and MPI libraries using Ubuntu 9.04 Synaptic Package Manager. What else should I do?<br>
I want to run a simulation in parallel on a single PC. Which commands should I enter the terminal?<br>
<br>
</blockquote>
<br></div>
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.<br>
<br>
For usage and instructions, see the manual and any of the numerous tutorials linked here:<br>
<br>
<a href="http://www.gromacs.org/Documentation/Tutorials#General" target="_blank">http://www.gromacs.org/Documentation/Tutorials#General</a><br>
<br>
-Justin<div><br>
<br>
<blockquote class="gmail_quote" style="border-left:1px solid rgb(204, 204, 204);margin:0pt 0pt 0pt 0.8ex;padding-left:1ex">
Thanks a lot for any instruction.<br>
<br>
<br>
</blockquote>
<br></div>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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