[gmx-users] Building executable for template.c!
Dear Users, I want to have executable file for template.c, but not in the default location and not during the installation of whole package. I am trying to do this for gromacs-4.6.5. When I use $cd /home/user/Documents/ $ tar xfz gromacs-4.6.5.tgz $ cd gromacs-4.6.5 $ mkdir build $ cd build $ cmake .. -DGMX_MPI=ON -DGMX_GPU=OFF -DGMX_BUILD_OWN_FFTW=ON -DGMX_DEFAULT_SUFFIX=ON -DGMX_DOUBLE=ON -DCMAKE_INSTALL_PREFIX=/home/user/gromacs4.6.5/ $ make install It installs gromacs package at /home/user/gromacs4.6.5/ and executable for template.c is at /home/user/Documents/gromacs4.6.5/build/share/template/. What I want to do is, I want to build the executable file for template not during the installation of whole package. I have copied the folder templatedistribution directory as /home/user/Documents/template/. Now I want to build the template using the already installed gromacs. I have renamed the CMakeLists.txt.template to CMakeLists.txt. Then did source /home/user/gromacs4.6.5/bin/GMXRC.bash. When I used cmake to build executable I end-up with either of the following error. -- checking for module 'libgmx_d' -- package 'libgmx_d' not found CMake Error at /usr/local/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:108 (message): Could NOT find GROMACS (missing: GROMACS_LIBRARY GROMACS_INCLUDE_DIR) or Could not find a package configuration file provided by GROMACS with any of the following names: GROMACSConfig.cmake gromacs-config.cmake Add the installation prefix of GROMACS to CMAKE_PREFIX_PATH or set GROMACS_DIR to a directory containing one of the above files. If GROMACS provides a separate development package or SDK, be sure it has been installed. Can anyone please guide me to build the executable for template.c in the different place using the already installed gromacs package. I think for the gromacs.4.5 this procedure is bit straight forward by changing the Makefile we can get it. But for gromacs-4.6.5 seems not so straight forward. Thanks in advance for your time and help. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Building executable for template.c!
I used Makefile instead of cmake. It is working now and I can build the executable as required. Thanks. On Sun, Nov 16, 2014 at 8:06 PM, Anjaiah Nalaparaju anjai@gmail.com wrote: Dear Users, I want to have executable file for template.c, but not in the default location and not during the installation of whole package. I am trying to do this for gromacs-4.6.5. When I use $cd /home/user/Documents/ $ tar xfz gromacs-4.6.5.tgz $ cd gromacs-4.6.5 $ mkdir build $ cd build $ cmake .. -DGMX_MPI=ON -DGMX_GPU=OFF -DGMX_BUILD_OWN_FFTW=ON -DGMX_DEFAULT_SUFFIX=ON -DGMX_DOUBLE=ON -DCMAKE_INSTALL_PREFIX=/home/user/gromacs4.6.5/ $ make install It installs gromacs package at /home/user/gromacs4.6.5/ and executable for template.c is at /home/user/Documents/gromacs4.6.5/build/share/template/. What I want to do is, I want to build the executable file for template not during the installation of whole package. I have copied the folder templatedistribution directory as /home/user/Documents/template/. Now I want to build the template using the already installed gromacs. I have renamed the CMakeLists.txt.template to CMakeLists.txt. Then did source /home/user/gromacs4.6.5/bin/GMXRC.bash. When I used cmake to build executable I end-up with either of the following error. -- checking for module 'libgmx_d' -- package 'libgmx_d' not found CMake Error at /usr/local/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:108 (message): Could NOT find GROMACS (missing: GROMACS_LIBRARY GROMACS_INCLUDE_DIR) or Could not find a package configuration file provided by GROMACS with any of the following names: GROMACSConfig.cmake gromacs-config.cmake Add the installation prefix of GROMACS to CMAKE_PREFIX_PATH or set GROMACS_DIR to a directory containing one of the above files. If GROMACS provides a separate development package or SDK, be sure it has been installed. Can anyone please guide me to build the executable for template.c in the different place using the already installed gromacs package. I think for the gromacs.4.5 this procedure is bit straight forward by changing the Makefile we can get it. But for gromacs-4.6.5 seems not so straight forward. Thanks in advance for your time and help. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Spherical Averaging (Debye formulation) in SAXS calculation!
Dear all, Anyone calculated SAXS profile using gmx saxs option. It is under g_rdf for gromacs 4.6.x version. My question is whether the spherical averaging has been implemented in this tool. I have checked the program, it seems spherical averaging is not implemented. Moreover, orientation of the solute molecule has effect on the SAXS profile calculated with this tool. For SANS calculation(g_sans), debye formulation is used to incorporate the spherical averaging. Why different methodology is adopted in SAXS and SANS calculation. Any clarification is greatly appreciated. Thanks in Advance. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
