Sathish wrote:
Dear Mark,
wow its working. Thank you lot.. As per installation instruction
gromacs installed successfully and demo also working.
Then i have downloaded test set "gmxtest-4.0.4.tgz". While running i got
error message like this,
[r...@xxx gmxtest]# ./gmxtest.pl <http://gmxtest.pl> all
FAILED. Check files in angles1
FAILED. Check files in angles125
FAILED. Check files in bham
FAILED. Check files in bonds1
FAILED. Check files in bonds125
FAILED. Check files in dih1
FAILED. Check files in dih125
FAILED. Check files in g96angles1
FAILED. Check files in g96angles125
FAILED. Check files in g96bonds1
FAILED. Check files in g96bonds125
FAILED. Check files in imp1
FAILED. Check files in imp36
FAILED. Check files in morse
FAILED. Check files in rb1
FAILED. Check files in rb125
16 out of 16 simple tests FAILED
FAILED. Check files in acetonitrilRF
FAILED. Check files in aminoacids
FAILED. Check files in argon
FAILED. Check files in butane
FAILED. Check files in dec+water
FAILED. Check files in ethyleenglycol
FAILED. Check files in fe_test
FAILED. Check files in field
FAILED. Check files in nacl
FAILED. Check files in sw
FAILED. Check files in tip4p
FAILED. Check files in tip4pflex
FAILED. Check files in urea
FAILED. Check files in water
14 out of 14 complex tests FAILED
FAILED. Check files in kernel020
FAILED. Check files in kernel120
FAILED. Check files in kernel121
FAILED. Check files in kernel122
FAILED. Check files in kernel123
FAILED. Check files in kernel124
FAILED. Check files in kernel220
FAILED. Check files in kernel221
FAILED. Check files in kernel222
FAILED. Check files in kernel223
FAILED. Check files in kernel224
FAILED. Check files in kernel320
FAILED. Check files in kernel321
FAILED. Check files in kernel322
FAILED. Check files in kernel323
FAILED. Check files in kernel324
16 out of 63 kernel tests FAILED
Error not all 45 pdb2gmx tests have been done successfully
Only 9 energies in the log file
[r...@xxx gmxtest]#
Could you explain what is exact problem and how to solve it?
1. The test set is not very robust, so failures are not necessarily indicative
of any actual problem.
2. You're using the 4.0.4 test set with version 4.5.1, so some failures are
probably due to new command line options, etc. (especially in the case of
pdb2gmx) being necessary but not invoked.
As it stands, there is no effective way to test the validity of a Gromacs
installation.
-Justin
On Wed, Oct 13, 2010 at 6:15 PM, David van der Spoel
<sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>> wrote:
On 2010-10-13 10.54, Sathish wrote:
Dear Mark,
I have one more doubt. How to run "luck". If i run luck
anywhere its says command not found..
my installed and binary directory cant find luck program. how to do?
without checking luck shall i start to run demo?
Instructions are outdated. The program is now called g_luck
On Wed, Oct 13, 2010 at 3:19 PM, Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>> wrote:
On 13/10/2010 5:01 PM, Mark Abraham wrote:
On 13/10/2010 4:55 PM, Sathish wrote:
Dear Mark,
Thanks for your reply. In my server gromacs
installed at
"local/gromacs". I have checked out point 8 as you
mentioned.
It was working with this "source
/local/gromacs/bin/GMXRC" command.
That's all you need to do, in every shell from which you
want to
use GROMACS. Or, put that command in your shell login scripts
(Google for details).
and also tried , entered "local/gromacs/bin" path and
calling to
GMXRC but it shows error
[r...@xxx bin]# GMXRC
/local/gromacs/bin/GMXRC: line 35: return: can only
`return' from
a function
or
sourced script
/local/gromacs/bin/GMXRC: line 44: CSH:: command not
found
/local/gromacs/bin/GMXRC.csh: line 8: syntax error near
unexpected token `setenv '
/local/gromacs/bin/GMXRC.csh: line 8: `if (!
$?LD_LIBRARY_PATH)
setenv
LD_LIBRAR
Y_PATH ""'
[r...@xxx bin]#
This doesn't work, and shouldn't.
And the only thing you should be doing as root are "make install"
and "make links" (if you want the latter). Otherwise you'll trash
your system before you know what you've done.
Mark
kindly help me to fix this problem and luck is not
working.
It should, if the "source" command worked.
Mark
On Wed, Oct 13, 2010 at 12:57 PM, Mark Abraham
<mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>> wrote:
----- Original Message -----
From: Sathish <sathisbioi...@gmail.com
<mailto:sathisbioi...@gmail.com>
<mailto:sathisbioi...@gmail.com
<mailto:sathisbioi...@gmail.com>>>
Date: Wednesday, October 13, 2010 14:31
Subject: [gmx-users] Gromacs installation problem
@ RHEL5.5
server
To: gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
> Dear all,
> I have compiled and installed gromacs 4.5.1 on
RHEL5.5
server. I have also installed openmpi-1.2.8,
fftw-3.2.2 and
gsl-1.11. After gromacs 4.5.1 installation did
make tests and
make links. Finally got message "GROMACS is
installed under
/root/software" and "binary executable installed
/usr/local/bin". Utill this am not getting any
errors.
> Then i was tried to calling "luck" but get
"command not
found".I have searched the forum it says binary
executable
not in your path.
> Am installing first time and need to know PATH
is right
which i given? Could anybody help me to solve
this problem?
> Advance thanks..
Check out point 8 of
http://www.gromacs.org/Downloads/Installation_Instructions
Mark
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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
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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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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