[gmx-users] How to compile Cygwin 4.6.3 for Windows using Cygwin
Hello, How to compile Cygwin 4.6.3 for Windows using Cygwin ? I did so: tar xfz gromacs-4.6.tar.gz cd gromacs-4.6 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON (fftw 3.3 - install) make Error message Thank you. -- 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] How to compile Cygwin 4.6.3 for Windows using Cygwin
Error message, аfter the make: In file included from /cygdrive/d/1/gromacs-4.6.3/src/gmxlib/thread_mpi/atomic.c:38:0: /cygdrive/d/1/gromacs-4.6.3/src/gmxlib/thread_mpi/impl.h:504:20: ошибка: field «timer_init» has incomplete type src/gmxlib/CMakeFiles/gmx.dir/build.make:8061: recipe for target `src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/atomic.c.o' failed make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/atomic.c.o] Error 1 CMakeFiles/Makefile2:1238: recipe for target `src/gmxlib/CMakeFiles/gmx.dir/all' failed make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 Makefile:146: recipe for target `all' failed make: *** [all] Error 2 On 7/14/13 1:04 PM, bh...@udsu.ru wrote: Hello, How to compile Cygwin 4.6.3 for Windows using Cygwin ? I did so: tar xfz gromacs-4.6.tar.gz cd gromacs-4.6 The version 4.6 tarball will not give you version 4.6.3 :) Unless this is a typo, make sure you're actually working with the newest version. mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON (fftw 3.3 - install) make Error message Please copy and paste the actual error message. Simply saying there's an error leaves it impossible to help you. -Justin -- 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] CygWin and Gromacs 4.5.5
Help me. I want to install Gromacs 4.5.5 with usage CygWin. When I execute a command make I receive the error report: numa_malloc.c:117: error: expected ' ' before ' Processor' numa_malloc.c:117: error: expected ' ' before ' ProcNumber' numa_malloc.c:117: error: expected ' = ', ', ', '; ', ' asm ' or. ... make [3]: *** [numa_malloc.lo] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib/thread_mpi' make [3]: *** [install-recursive] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib' make [3]: *** [install-recursive] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src' make [3]: *** [install-recursive] Error 1 Where an error? CygWin it is installed with packets: Section Devel - autoconf: Wrapper scripts for autoconf commands - autoconf2.1: Stable version of the automatic configure script builder - autoconf2.5: Development version of the automatic configure script builder - automake1.9: a tool for generating GNU-compliant Makefiles - binutils: The GNU assembler, linker and binary utilites - gcc: A C compiler upgrade helper - gcc-core: A C compiler - gcc-g ++: A C ++ compiler - gcc-g77: Fortran compiler - gcc-mingw-core: Mingw32 support headers and libraries for GCC - gcc-mingw-g ++: Mingw32 support headers and libraries for GCC A C ++ - gcc-mingw-g77: Mingw32 support headers and libraries for GCC Fortran - libgcc1: GCC compiler support shared runtime - libgdbm-devel: GNU dbm database routines (development) - make: The GNU version of the ` make ` utility - mingw-runtime: MinGW Runtime Section Interpreters - perl: Larry Wall ` s Practical Extracting and Report Language Packet FFTW ver.3.2.2 is in addition compiled and installed Trial setting Gromacs of 4.5.3 errors does not give. The instruction on setting took here: http://lists.groma cs.org/pipermail/gmx-users/2009-September/044792.html The error arises only for version Gromacs 4.5.5 Igor -- 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] CygWin and Gromacs 4.5.5
I have read and have carried out the instruction on the given page. The error arises again. Igor В письме от Втр, 08 Ноя 2011, 16:35 Szilárd Páll пишет: Hi, There have been quite some discussion on the topic of GROMACS on Cygwin so please search the mailing list for information. Some of that information might have not gone into the wiki (http://goo.gl/ALQuC) - especially that the page appears to be intact for the last 7 months. [Which is a pity and it would be really much appreciated if people in the future contribute back!!!] Additionally, AFAIK you will get better performance if you compile with MSVC which should be fairly easy if you use CMake - I'm not entirely sure about this though. Cheers, -- Szilárd On Tue, Nov 8, 2011 at 12:41 PM, bh...@udsu.ru wrote: Help me. I want to install Gromacs 4.5.5 with usage CygWin. When I execute a command make I receive the error report: numa_malloc.c:117: error: expected ' ' before ' Processor' numa_malloc.c:117: error: expected ' ' before ' ProcNumber' numa_malloc.c:117: error: expected ' = ', ', ', '; ', ' asm ' or. ... make [3]: *** [numa_malloc.lo] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib/thread_mpi' make [3]: *** [install-recursive] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib' make [3]: *** [install-recursive] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src' make [3]: *** [install-recursive] Error 1 Where an error? CygWin it is installed with packets: Section Devel - autoconf: Wrapper scripts for autoconf commands - autoconf2.1: Stable version of the automatic configure script builder - autoconf2.5: Development version of the automatic configure script builder - automake1.9: a tool for generating GNU-compliant Makefiles - binutils: The GNU assembler, linker and binary utilites - gcc: A C compiler upgrade helper - gcc-core: A C compiler - gcc-g ++: A C ++ compiler - gcc-g77: Fortran compiler - gcc-mingw-core: Mingw32 support headers and libraries for GCC - gcc-mingw-g ++: Mingw32 support headers and libraries for GCC A C ++ - gcc-mingw-g77: Mingw32 support headers and libraries for GCC Fortran - libgcc1: GCC compiler support shared runtime - libgdbm-devel: GNU dbm database routines (development) - make: The GNU version of the ` make ` utility - mingw-runtime: MinGW Runtime Section Interpreters - perl: Larry Wall ` s Practical Extracting and Report Language Packet FFTW ver.3.2.2 is in addition compiled and installed Trial setting Gromacs of 4.5.3 errors does not give. The instruction on setting took here: http://lists.groma cs.org/pipermail/gmx-users/2009-September/044792.html The error arises only for version Gromacs 4.5.5 Igor -- gmx-users mailing list gmx-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 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 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] OPLS for group -N=CH2
Dear users. Help me. What parametres of force field OPLS it is necessary to be used for group -N=CH2 (imine group) ? The best regards, Igor -- 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] extrnal itp files
Could you tell me, please. What's directions need the programm pdb2gmx to use external .itp files, for example martini_v2.1.itp (Coarse Grained Force Field)? How is it to do ? I use GROMACS v3.3.2 and OPLSAA Force Field. Igor ___ 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: Re: [gmx-users] extrnal itp files
It is possible to set an example ? bhf70 wrote: Could you tell me, please. What's directions need the programm pdb2gmx to use external .itp files, for example martini_v2.1.itp (Coarse Grained Force Field)? How is it to do ? There should be instructions accompanying that force field wherever you got it from. There's some general information here http://wiki.gromacs.org/index.php/Include_File_Mechanism 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 . ___ 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
