gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote:
Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than "Re: Contents of gromacs.org_gmx-users digest..." Today's Topics: 1. Regarding structure analysis of DNA (Sathish Kumar) 2. Set the environment variables of "FFTW3_INCLUDE_DIR" and "FFTW3_LIBRARIES" (Hassan Aaryapour) ---------------------------------------------------------------------- Message: 1 Date: Mon, 3 Mar 2014 01:05:41 -0800 From: Sathish Kumar <sathishk...@gmail.com> To: Discussion list for GROMACS users <gmx-us...@gromacs.org> Subject: [gmx-users] Regarding structure analysis of DNA Message-ID: <CAFi=hwk79kpmzoy9nceko+qf+9xummuztwoya8pmragbnhb...@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hai I have done simulation of DNA on carbon nano tube surface. I want to calculate structural changes (means changes in stacking, puckering angles and bending of helix) in DNA. Can any suggest me how to calculate these things. Thank You Very Much. regards M.SathishKumar ------------------------------ Message: 2 Date: Mon, 3 Mar 2014 13:56:01 +0330 From: Hassan Aaryapour <hassan.grom...@gmail.com> To: "gromacs.org_gmx-users" <gromacs.org_gmx-users@maillist.sys.kth.se> Subject: [gmx-users] Set the environment variables of "FFTW3_INCLUDE_DIR" and "FFTW3_LIBRARIES" Message-ID: <cacqaq9-nsm-extkcpwyr6khr1+0t75x4nw0mbrunlxhc_eh...@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Dear Gmx-user; I want to install double precision gromacs 4.5.3 and FFTW 3.3.2 in my home directory. first, according to the FFTW installation instructions I installed and introduced it to bash shell it as the following order: $tar -xzvf fftw-3.3.2.tar.gz $./configure --enable-threads --prefix=/home/WeNMR/ProgramFiles/fftw $make $make install export CPPFLAGS=-I/home/WeNMR/ProgramFiles/fftw/include export LDFLAGS=-L/home/WeNMR/ProgramFiles/fftw/lib but it isn't found automatically by cmake when I want to install gromacs. and this error was appeared: CMake Error at /usr/local/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:108 (message): Could not find FFTW3. Provide the fftw3 install directory in the FFTW3_ROOT_DIR environment variable. (missing: FFTW3_LIBRARIES FFTW3_INCLUDE_DIR) Call Stack (most recent call first): /usr/local/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:315 (_FPHSA_FAILURE_MESSAGE) cmake/FindFFTW3.cmake:31 (find_package_handle_standard_args) CMakeLists.txt:636 (find_package) How can I set the environment variables for "FFTW3_INCLUDE_DIR" and "FFTW3_LIBRARIES"? can I add my FFTW installed path to "CMakeLists.txt" file in the related section in below? how? if(${GMX_FFT_LIBRARY} STREQUAL "FFTW3") # MESSAGE(STATUS "Using external FFT library - fftw3") if(GMX_DOUBLE) find_package(FFTW3 REQUIRED) include_directories(${FFTW3_INCLUDE_DIR}) set(FFT_LIBRARIES ${FFTW3_LIBRARIES}) set(PKG_FFT "fftw3") else(GMX_DOUBLE) find_package(FFTW3F REQUIRED) include_directories(${FFTW3F_INCLUDE_DIR}) set(FFT_LIBRARIES ${FFTW3F_LIBRARIES}) set(PKG_FFT "fftw3f") endif(GMX_DOUBLE) Thank you in advance Hassan ------------------------------ -- 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. End of gromacs.org_gmx-users Digest, Vol 119, Issue 8 ***************************************************** -- 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.