RE: [gmx-users] Question about the Gromacs website
Just accessed it. Stephen P. Molnar, Ph.D.Life is a fuzzy set Foundation for ChemistryStochastic and multivariate www.FoundationForChemistry.com (614)312-7528 (c) Skype: smolnar1 -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Andrew DeYoung Sent: Sunday, July 15, 2012 2:00 PM To: gmx-users@gromacs.org Subject: [gmx-users] Question about the Gromacs website Hi, I have been not been able to access http://www.gromacs.org/ today. Has anyone else experienced this? I received the following error message on both Google Chrome and Mozilla Firefox: -- Site settings could not be loaded We were unable to locate the API to request site settings. Please see below for debugging information. If this is a new install, try refreshing - the API is simply taking its time loading up! HTTP Response Status Code: 500 -- Best wishes, Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Problem Compiling grogui with plotting.
openSUSE 12.1 64bit. I have managed to compile grogui with plotting on earlier versions of openSUSE. However when I attempt compiling the program on my current OS I get the following errors: src/editor.cpp: In member function ‘void Editor::updateMenus()’: src/editor.cpp:156:59: error: ‘class MdiChild’ has no member named ‘isUndoAvailable’ src/editor.cpp:157:59: error: ‘class MdiChild’ has no member named ‘isRedoAvailable’ make: *** [editor.o] Error 1 The complete make.log is attached. Any assistance will be appreciated. Thanks in advance. -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivariate http://www.FoundationForChemistry.com (614)312-7528 (c) Skype: smolnar1 computation@linux-iq76:~/Downloads/ggui/grogui052/gui_withplotting> qmake computation@linux-iq76:~/Downloads/ggui/grogui052/gui_withplotting> make Makefile:518: warning: overriding recipe for target `qrc_main.cpp' Makefile:422: warning: ignoring old recipe for target `qrc_main.cpp' Makefile:536: warning: overriding recipe for target `qrc_mdi.cpp' Makefile:440: warning: ignoring old recipe for target `qrc_mdi.cpp' g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/default -I. -I/usr/include/QtCore -I/usr/include/QtGui -I/usr/include -I. -Iinclude -Iui -I/usr/include/qwt5 -I. -o plotwidget.o src/plotwidget.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/default -I. -I/usr/include/QtCore -I/usr/include/QtGui -I/usr/include -I. -Iinclude -Iui -I/usr/include/qwt5 -I. -o finddialog.o src/finddialog.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/default -I. -I/usr/include/QtCore -I/usr/include/QtGui -I/usr/include -I. -Iinclude -Iui -I/usr/include/qwt5 -I. -o iconprovider.o src/iconprovider.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/default -I. -I/usr/include/QtCore -I/usr/include/QtGui -I/usr/include -I. -Iinclude -Iui -I/usr/include/qwt5 -I. -o aboutgrogui.o src/aboutgrogui.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/default -I. -I/usr/include/QtCore -I/usr/include/QtGui -I/usr/include -I. -Iinclude -Iui -I/usr/include/qwt5 -I. -o addpopupitem.o src/addpopupitem.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/default -I. -I/usr/include/QtCore -I/usr/include/QtGui -I/usr/include -I. -Iinclude -Iui -I/usr/include/qwt5 -I. -o commands.o src/commands.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/default -I. -I/usr/include/QtCore -I/usr/include/QtGui -I/usr/include -I. -Iinclude -Iui -I/usr/include/qwt5 -I. -o dirbrowser.o src/dirbrowser.cpp src/dirbrowser.cpp: In member function âQModelIndex DirBrowser::indexAt(const QPoint&) constâ: src/dirbrowser.cpp:161:1: warning: no return statement in function returning non-void [-Wreturn-ty src/dirbrowser.cpp: At global scope: src/dirbrowser.cpp:158:13: warning: unused parameter âpointâ [-Wunused-parameter] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/include/qwt5 -I. -o editor.o src/editor.cpp src/editor.cpp: In member function âvoid Editor::updateMenus()â: src/editor.cpp:156:59: error: âclass MdiChildâ has no member named âisUndoAvailableâ src/editor.cpp:157:59: error: âclass MdiChildâ has no member named âisRedoAvailableâ make: *** [editor.o] Error 1 computation@linux-iq76:~/Downloads/ggui/grogui052/gui_withplotting> -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Problem Installing 4.5.1
OpenSuSE 11.2 on 64bit AMD computer. Compiling and installation went smoothly without any warning or error messages. However, when I attempted running gmxdemo, the execution hund in pdb2gmx, the output file is attached. Any help will be much appreciated. Thanks in advance. -- Stephen P. Molnar, Ph.D.Life is a fuzzy set Foundation for ChemistryStochastic and multivarate http://www.FoundationForChemistry.com output.pdb2gmx Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gtkmm Code Demos?
Thank you for your response to my most recet post. I did compile without the --enable-shared and got the same result. Mark Abraham wrote: Stephen P. Molnar wrote: The demo to which I was referring is /sdb5/Applications/gromacs/share/gromacs/tutor/gmxdemo (sorry about that, it was a direct result of my memory) The configure command line that I used was "configure --prefix=/sdb5/Applications/gromacs --exec-prefix=/sdb5/Applications/gromacs --enable-shared" and searching the configure .log does not come up with gtkmm. I rather wonder why gtkmm was invoked by the compilation process. Since gtkmm relates to widget-style display, and the only part of GROMACS that uses X is ngmx (which is used by gmxdemo) then my best suggestion is that you've got some mangled X environment that didn't link properly. Perhaps you can confirm that from the output of gmxdemo and the point at which it fails. You should also try configure without --enable-shared, since it might be a linking problem. You can also configure GROMACS --without-x, but that will mean gmxdemo can't run correctly. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- -- Stephen P. Molnar, Ph.D.Life is a fuzzy set Foundation for ChemistryStochastic and multivariate http://www.geocities.com/FoundationForChemistry ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gtkmm Code Demos?
The demo to which I was referring is /sdb5/Applications/gromacs/share/gromacs/tutor/gmxdemo (sorry about that, it was a direct result of my memory) The configure command line that I used was "configure --prefix=/sdb5/Applications/gromacs --exec-prefix=/sdb5/Applications/gromacs --enable-shared" and searching the configure .log does not come up with gtkmm. I rather wonder why gtkmm was invoked by the compilation process. Mark Abraham wrote: Stephen P. Molnar wrote: Due to an unfortunate loss of my working copy I have had to recompile gromacs-4.0.4 on my OpenSuSE 10.3 computer. I encountered no problems but when I attempt to run demo I get a popup box labeled gtkmm Code Demos. This is accompanied by an error message "** (demo:19437): WARNING **: Cannot open example_appwindow.cc: No such file or directory". What "demo" do you mean? I have been using gromacs through quite a number of versions over the years but have never encounteded this before. I searched both web and the gromacs.org site and can't find anything gtkmm (http://www.gtkmm.org/) is something that doesn't have any business with GROMACS. However you've configured and built GROMACS is probably unsuitable. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- -- Stephen P. Molnar, Ph.D.Life is a fuzzy set Foundation for ChemistryStochastic and multivariate http://www.geocities.com/FoundationForChemistry ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gtkmm Code Demos?
Due to an unfortunate loss of my working copy I have had to recompile gromacs-4.0.4 on my OpenSuSE 10.3 computer. I encountered no problems but when I attempt to run demo I get a popup box labeled gtkmm Code Demos. This is accompanied by an error message "** (demo:19437): WARNING **: Cannot open example_appwindow.cc: No such file or directory". I have been using gromacs through quite a number of versions over the years but have never encounteded this before. I searched both web and the gromacs.org site and can't find anything I would appreciate some pointers in the right direction. Thanks in advance. -- -- Stephen P. Molnar, Ph.D.Life is a fuzzy set Foundation for ChemistryStochastic and multivariate http://www.geocities.com/FoundationForChemistry ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem with 4.0.3
David van der Spoel wrote:
Stephen P. Molnar wrote:
David van der Spoel wrote:
Stephen P. Molnar wrote:
I have just downloaded and installed 4.0.3. I received neither
warning nor error during the process. However when I attempt to
run the gmxdemo I get:
Fatal error:
Library file F.dat not found in current dir nor in default directories
each successive step in demo gets a corresponding error message.
Yet the 'missing' files, e.g. FF.dat are in
/sdb5/Applications/gromacs/share/gromacs/top
Here is what I put in my .bashrc file:
##
# This is the real configuration part. We save the Gromacs
# things in separate vars, so we can remove them later.
# If you move gromacs, change the next four line.
##
GMXBIN=/sdb5/Applications/gromacs/bin
GMXLDLIB=/sdb5/Applications/gromacs/lib
GMXMAN=/sdb5/Applications/gromacs/share/man
GMXDATA=/sdb5/Applications/gromacs/share
# NB: The variables already begin with ':' now, or are empty
LD_LIBRARY_PATH=${GMXLDLIB}${LD_LIBRARY_PATH}
PATH=${GMXBIN}${PATH}
MANPATH=${GMXMAN}${MANPATH}
Try:
. /sdb5/Applications/gromacs/bin/GMXRC
# export should be separate, so /bin/sh understands it
export GMXBIN GMXLDLIB GMXMAN GMXDATA LD_LIBRARY_PATH PATH MANPATH
Obviously I've installed gromacs in a non-default location. What
modifications should I make, I presume to .cashrc, so that the
necessary files will be found?
Thanks in advance.
--
Stephen P. Molnar, Ph.D.Life is a fuzzy set
Foundation for ChemistryStochastic and multivariate
http://www.geocities.com/FoundationForChemistry
___
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Thanks for the suggestion. Here is the result:
computat...@abnormal:/sdb5/Applications/gromacs/share/gromacs/tutor/gmxdemo>
/sdb5/Applications/gromacs/bin/GMXRC
/sdb5/Applications/gromacs/bin/GMXRC: line 35: return: can only
`return' from a function or sourced script
/sdb5/Applications/gromacs/bin/GMXRC: line 44: CSH:: command not found
/sdb5/Applications/gromacs/bin/GMXRC.csh: line 8: syntax error near
unexpected token `setenv'
/sdb5/Applications/gromacs/bin/GMXRC.csh: line 8: `if (!
$?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ""'
computat...@abnormal:/sdb5/Applications/gromacs/share/gromacs/tutor/gmxdemo>
You forgot the leading period ( . )
That is what I classify as a red faced forehead slapper.
Many thanks. All is now well.
--
--
Stephen P. Molnar, Ph.D.Life is a fuzzy set
Foundation for ChemistryStochastic and multivariate
http://www.geocities.com/FoundationForChemistry
___
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http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] Problem with 4.0.3
David van der Spoel wrote:
Stephen P. Molnar wrote:
I have just downloaded and installed 4.0.3. I received neither
warning nor error during the process. However when I attempt to run
the gmxdemo I get:
Fatal error:
Library file F.dat not found in current dir nor in default directories
each successive step in demo gets a corresponding error message. Yet
the 'missing' files, e.g. FF.dat are in
/sdb5/Applications/gromacs/share/gromacs/top
Here is what I put in my .bashrc file:
##
# This is the real configuration part. We save the Gromacs
# things in separate vars, so we can remove them later.
# If you move gromacs, change the next four line.
##
GMXBIN=/sdb5/Applications/gromacs/bin
GMXLDLIB=/sdb5/Applications/gromacs/lib
GMXMAN=/sdb5/Applications/gromacs/share/man
GMXDATA=/sdb5/Applications/gromacs/share
# NB: The variables already begin with ':' now, or are empty
LD_LIBRARY_PATH=${GMXLDLIB}${LD_LIBRARY_PATH}
PATH=${GMXBIN}${PATH}
MANPATH=${GMXMAN}${MANPATH}
Try:
. /sdb5/Applications/gromacs/bin/GMXRC
# export should be separate, so /bin/sh understands it
export GMXBIN GMXLDLIB GMXMAN GMXDATA LD_LIBRARY_PATH PATH MANPATH
Obviously I've installed gromacs in a non-default location. What
modifications should I make, I presume to .cashrc, so that the
necessary files will be found?
Thanks in advance.
--
Stephen P. Molnar, Ph.D.Life is a fuzzy set
Foundation for ChemistryStochastic and multivariate
http://www.geocities.com/FoundationForChemistry
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
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interface or send it to gmx-users-requ...@gromacs.org.
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Thanks for the suggestion. Here is the result:
computat...@abnormal:/sdb5/Applications/gromacs/share/gromacs/tutor/gmxdemo>
/sdb5/Applications/gromacs/bin/GMXRC
/sdb5/Applications/gromacs/bin/GMXRC: line 35: return: can only `return'
from a function or sourced script
/sdb5/Applications/gromacs/bin/GMXRC: line 44: CSH:: command not found
/sdb5/Applications/gromacs/bin/GMXRC.csh: line 8: syntax error near
unexpected token `setenv'
/sdb5/Applications/gromacs/bin/GMXRC.csh: line 8: `if (!
$?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ""'
computat...@abnormal:/sdb5/Applications/gromacs/share/gromacs/tutor/gmxdemo>
--
--
Stephen P. Molnar, Ph.D.Life is a fuzzy set
Foundation for ChemistryStochastic and multivariate
http://www.geocities.com/FoundationForChemistry
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problem with 4.0.3
I have just downloaded and installed 4.0.3. I received neither warning
nor error during the process. However when I attempt to run the gmxdemo
I get:
Fatal error:
Library file F.dat not found in current dir nor in default directories
each successive step in demo gets a corresponding error message. Yet
the 'missing' files, e.g. FF.dat are in
/sdb5/Applications/gromacs/share/gromacs/top
Here is what I put in my .bashrc file:
##
# This is the real configuration part. We save the Gromacs
# things in separate vars, so we can remove them later.
# If you move gromacs, change the next four line.
##
GMXBIN=/sdb5/Applications/gromacs/bin
GMXLDLIB=/sdb5/Applications/gromacs/lib
GMXMAN=/sdb5/Applications/gromacs/share/man
GMXDATA=/sdb5/Applications/gromacs/share
# NB: The variables already begin with ':' now, or are empty
LD_LIBRARY_PATH=${GMXLDLIB}${LD_LIBRARY_PATH}
PATH=${GMXBIN}${PATH}
MANPATH=${GMXMAN}${MANPATH}
# export should be separate, so /bin/sh understands it
export GMXBIN GMXLDLIB GMXMAN GMXDATA LD_LIBRARY_PATH PATH MANPATH
Obviously I've installed gromacs in a non-default location. What
modifications should I make, I presume to .cashrc, so that the necessary
files will be found?
Thanks in advance.
--
Stephen P. Molnar, Ph.D.Life is a fuzzy set
Foundation for ChemistryStochastic and multivariate
http://www.geocities.com/FoundationForChemistry
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
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[gmx-users] Permissions Problems with a New Installation
I have just upgraded my linux computer with a 64 bit AMD CPU running the 64 bit openSUSW 10.2. I installed the appropriate version of gromacs in the installer default locations as the superuser without any problems. When I run the demo as a user there appear to be permissions issues. First of all, everytime the demo script opens a xterm window it flashes and closes. Here's what I get when the demo script gets to the grimpp module: generating energy minimisation parameter file... em.mdp: Permission denied. Starting grompp... [1] 14663 [1]Done xterm -title grompp -sb -e tail +0f output.grompp_em output.grompp_em: Permission denied. grompp finished Press Then the demo script ends on: e are finished simulating, and we are going to view the calculated trajectory. The trajectory file ( .trj extension ) contains all coordinates, velocities and forces of all the atoms in our system. The next program we are going run is ngmx. ngmx is a very simple trajectory viewer. Once the ngmx program has been started you need to click on a few buttons to view your trajectory. 1. Once the program has been started a dialog box shows up. Click on the box on the left of the word Protein. ( This means that we want to view the peptide ). Then Click on the OK Button 2. Now we see the edges of the box with a lines drawing of the peptide we just simulated. 3. Select Animation in the Display menu. If you did this correctly. A dialog box at the bottom of the screen appears. This dialog box is used to move through your trajectory. 4. Click on the FastForward button (two triangles pointing to the right) and watch the peptide moving. - - Starting Trajectory viewer... ngmx: Command not found. [1] 14724 [1]Exit 1ngmx -f cpeptide_md -s cpeptide_md tutor/gmxdemo> I will be most appreciative of assistance in solving this problem as permissions as a user remain a black, arcane mystery to me. Thanks in advance. -- Stephen P. Molnar, Ph.D.Life is a fuzzy set Foundation for ChemistryStochastic and multivariate http://www.geocities.com/FoundationForChemistry ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
