Dear Mark,<br><br> wow its working. Thank you lot.. As per installation instruction gromacs installed successfully and demo also working.<br>Then i have downloaded test set "gmxtest-4.0.4.tgz". While running i got error message like this,<br>
<br>[root@XXX gmxtest]# ./<a href="http://gmxtest.pl">gmxtest.pl</a> all<br>FAILED. Check files in angles1<br>FAILED. Check files in angles125<br>FAILED. Check files in bham<br>FAILED. Check files in bonds1<br>FAILED. Check files in bonds125<br>
FAILED. Check files in dih1<br>FAILED. Check files in dih125<br>FAILED. Check files in g96angles1<br>FAILED. Check files in g96angles125<br>FAILED. Check files in g96bonds1<br>FAILED. Check files in g96bonds125<br>FAILED. Check files in imp1<br>
FAILED. Check files in imp36<br>FAILED. Check files in morse<br>FAILED. Check files in rb1<br>FAILED. Check files in rb125<br>16 out of 16 simple tests FAILED<br>FAILED. Check files in acetonitrilRF<br>FAILED. Check files in aminoacids<br>
FAILED. Check files in argon<br>FAILED. Check files in butane<br>FAILED. Check files in dec+water<br>FAILED. Check files in ethyleenglycol<br>FAILED. Check files in fe_test<br>FAILED. Check files in field<br>FAILED. Check files in nacl<br>
FAILED. Check files in sw<br>FAILED. Check files in tip4p<br>FAILED. Check files in tip4pflex<br>FAILED. Check files in urea<br>FAILED. Check files in water<br>14 out of 14 complex tests FAILED<br>FAILED. Check files in kernel020<br>
FAILED. Check files in kernel120<br>FAILED. Check files in kernel121<br>FAILED. Check files in kernel122<br>FAILED. Check files in kernel123<br>FAILED. Check files in kernel124<br>FAILED. Check files in kernel220<br>FAILED. Check files in kernel221<br>
FAILED. Check files in kernel222<br>FAILED. Check files in kernel223<br>FAILED. Check files in kernel224<br>FAILED. Check files in kernel320<br>FAILED. Check files in kernel321<br>FAILED. Check files in kernel322<br>FAILED. Check files in kernel323<br>
FAILED. Check files in kernel324<br>16 out of 63 kernel tests FAILED<br>Error not all 45 pdb2gmx tests have been done successfully<br>Only 9 energies in the log file<br>[root@XXX gmxtest]#<br> <br>Could you explain what is exact problem and how to solve it?<br>
<br> <br><br><div class="gmail_quote">On Wed, Oct 13, 2010 at 6:15 PM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im">On 2010-10-13 10.54, Sathish wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear Mark,<br>
<br>
I have one more doubt. How to run "luck". If i run luck<br>
anywhere its says command not found..<br>
my installed and binary directory cant find luck program. how to do?<br>
without checking luck shall i start to run demo?<br>
<br>
</blockquote></div>
Instructions are outdated. The program is now called g_luck<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">
<br>
<br>
On Wed, Oct 13, 2010 at 3:19 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br></div><div><div></div><div class="h5">
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>> wrote:<br>
<br>
On 13/10/2010 5:01 PM, Mark Abraham wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
On 13/10/2010 4:55 PM, Sathish wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear Mark,<br>
Thanks for your reply. In my server gromacs installed at<br>
"local/gromacs". I have checked out point 8 as you mentioned.<br>
It was working with this "source /local/gromacs/bin/GMXRC" command.<br>
</blockquote>
<br>
That's all you need to do, in every shell from which you want to<br>
use GROMACS. Or, put that command in your shell login scripts<br>
(Google for details).<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
and also tried , entered "local/gromacs/bin" path and calling to<br>
GMXRC but it shows error<br>
<br>
[root@xxx bin]# GMXRC<br>
/local/gromacs/bin/GMXRC: line 35: return: can only `return' from<br>
a function<br>
or<br>
sourced script<br>
/local/gromacs/bin/GMXRC: line 44: CSH:: command not found<br>
/local/gromacs/bin/GMXRC.csh: line 8: syntax error near<br>
unexpected token `setenv '<br>
/local/gromacs/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH)<br>
setenv<br>
LD_LIBRAR<br>
Y_PATH ""'<br>
[root@xxx bin]#<br>
</blockquote>
This doesn't work, and shouldn't.<br>
</blockquote>
And the only thing you should be doing as root are "make install"<br>
and "make links" (if you want the latter). Otherwise you'll trash<br>
your system before you know what you've done.<br>
<br>
Mark<br>
<br>
</div></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div class="h5"><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
kindly help me to fix this problem and luck is not working.<br>
</blockquote>
It should, if the "source" command worked.<br>
<br>
Mark<br>
</div></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div class="h5">
<br>
<br>
<br>
<br>
On Wed, Oct 13, 2010 at 12:57 PM, Mark Abraham<br></div></div><div class="im">
<<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a> <mailto:<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>>> wrote:<br>
<br>
<br>
<br>
----- Original Message -----<br>
From: Sathish <<a href="mailto:sathisbioinfo@gmail.com" target="_blank">sathisbioinfo@gmail.com</a><br></div><div class="im">
<mailto:<a href="mailto:sathisbioinfo@gmail.com" target="_blank">sathisbioinfo@gmail.com</a>>><br>
Date: Wednesday, October 13, 2010 14:31<br>
Subject: [gmx-users] Gromacs installation problem @ RHEL5.5<br>
server<br></div><div class="im">
To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
<br>
> Dear all,<br>
> I have compiled and installed gromacs 4.5.1 on RHEL5.5<br>
server. I have also installed openmpi-1.2.8, fftw-3.2.2 and<br>
gsl-1.11. After gromacs 4.5.1 installation did make tests and<br>
make links. Finally got message "GROMACS is installed under<br>
/root/software" and "binary executable installed<br>
/usr/local/bin". Utill this am not getting any errors.<br>
> Then i was tried to calling "luck" but get "command not<br>
found".I have searched the forum it says binary executable<br>
not in your path.<br>
> Am installing first time and need to know PATH is right<br>
which i given? Could anybody help me to solve this problem?<br>
> Advance thanks..<br>
<br>
Check out point 8 of<br>
<a href="http://www.gromacs.org/Downloads/Installation_Instructions" target="_blank">http://www.gromacs.org/Downloads/Installation_Instructions</a><br>
<br>
Mark<br>
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<br>
<br>
<br>
<br>
--<br>
--<br>
Regards,<br>
N. Sathishkumar,<br>
<br>
</div></blockquote>
<br>
</blockquote><div class="im">
<br>
<br>
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<br>
--<br>
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Regards,<br>
N. Sathishkumar,<br>
<br>
</div></blockquote>
<br>
<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br><font color="#888888">
-- <br></font><div><div></div><div class="h5">
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>-- <br>Regards,<br>N. Sathishkumar,<br><br>