subject:"Re\: \[gmx\-users\] Installation error"

Re: [gmx-users] Installation error

2018-03-24 Thread Mark Abraham

Hi,

No. You said you have fftw 3.3.7 so just let the cmake you have use it :-)

Mark

On Sat, Mar 24, 2018, 18:49 ali akgün  wrote:

> Should i use another version of cmake ?
> On Sat, Mar 24, 2018 at 3:05 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > If you have fftw 3.3.7, then you don't need to ask the GROMACS build
> system
> > to download and build fftw for you. The error is suggesting that the
> issue
> > is that your CMake build wasn't configured to be able to do the download
> > that your asking GROMACS to ask CMake to do.
> >
> > Mark
> >
> > On Sat, Mar 24, 2018, 12:28 ali akgün  wrote:
> >
> > > Hello,
> > >
> > > I got an error in gromacs-5.0.7 installiation cmake part.
> > >
> > > My error is:
> > >
> > >
> > > Scanning dependencies of target fftwBuild
> > > Scanning dependencies of target mdrun_objlib
> > > Scanning dependencies of target view_objlib
> > > [  0%] Performing pre-download step for 'fftwBuild'
> > > [  0%] Creating directories for 'fftwBuild'
> > > -- downloading...
> > >  src='http://www.fftw.org/fftw-3.3.3.tar.gz'
> > >
> > > dest='/home/ali/Downloads/gromacs-5.0.7/build/src/
> > contrib/fftw/fftw.tar.gz'
> > > CMake Error at fftw-download.cmake:9 (file):
> > >   file DOWNLOAD not supported by bootstrap cmake.
> > >
> > >
> > > src/contrib/fftw/CMakeFiles/fftwBuild.dir/build.make:119: recipe for
> > target
> > >
> > > 'src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/
> > fftwBuild-pre-download'
> > > failed
> > > make[2]: ***
> > >
> > > [src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/
> > fftwBuild-pre-download]
> > > Error 1
> > > make[2]: *** Waiting for unfinished jobs
> > > CMakeFiles/Makefile2:1124: recipe for target
> > > 'src/contrib/fftw/CMakeFiles/fftwBuild.dir/all' failed
> > > make[1]: *** [src/contrib/fftw/CMakeFiles/fftwBuild.dir/all] Error 2
> > > make[1]: *** Waiting for unfinished jobs
> > > [  1%] Building CXX object
> > > src/programs/CMakeFiles/view_objlib.dir/view/view.cpp.o
> > > [  1%] Built target view_objlib
> > > [  1%] Building C object
> > > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/md.c.o
> > > [  2%] Building C object
> > > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/membed.c.o
> > > [  2%] Building C object
> > > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/pme_loadbal.c.o
> > > [  2%] Building C object
> > > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/repl_ex.c.o
> > > [  2%] Building CXX object
> > > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o
> > > [  2%] Building C object
> > > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/runner.c.o
> > > [  2%] Built target mdrun_objlib
> > > Makefile:162: recipe for target 'all' failed
> > > make: *** [all] Error 2
> > >
> > >
> > > How to fix this error?
> > >
> > > Cmake version is 3.11.0
> > > FFTW version is 3.3.7
> > >
> > > Thank you.
> > > --
> > > 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.
> > >
> > --
> > 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.
> --
> 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.
-- 
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Re: [gmx-users] Installation error

2018-03-24 Thread ali akgün

Should i use another version of cmake ?
On Sat, Mar 24, 2018 at 3:05 PM, Mark Abraham 
wrote:

> Hi,
>
> If you have fftw 3.3.7, then you don't need to ask the GROMACS build system
> to download and build fftw for you. The error is suggesting that the issue
> is that your CMake build wasn't configured to be able to do the download
> that your asking GROMACS to ask CMake to do.
>
> Mark
>
> On Sat, Mar 24, 2018, 12:28 ali akgün  wrote:
>
> > Hello,
> >
> > I got an error in gromacs-5.0.7 installiation cmake part.
> >
> > My error is:
> >
> >
> > Scanning dependencies of target fftwBuild
> > Scanning dependencies of target mdrun_objlib
> > Scanning dependencies of target view_objlib
> > [  0%] Performing pre-download step for 'fftwBuild'
> > [  0%] Creating directories for 'fftwBuild'
> > -- downloading...
> >  src='http://www.fftw.org/fftw-3.3.3.tar.gz'
> >
> > dest='/home/ali/Downloads/gromacs-5.0.7/build/src/
> contrib/fftw/fftw.tar.gz'
> > CMake Error at fftw-download.cmake:9 (file):
> >   file DOWNLOAD not supported by bootstrap cmake.
> >
> >
> > src/contrib/fftw/CMakeFiles/fftwBuild.dir/build.make:119: recipe for
> target
> >
> > 'src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/
> fftwBuild-pre-download'
> > failed
> > make[2]: ***
> >
> > [src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/
> fftwBuild-pre-download]
> > Error 1
> > make[2]: *** Waiting for unfinished jobs
> > CMakeFiles/Makefile2:1124: recipe for target
> > 'src/contrib/fftw/CMakeFiles/fftwBuild.dir/all' failed
> > make[1]: *** [src/contrib/fftw/CMakeFiles/fftwBuild.dir/all] Error 2
> > make[1]: *** Waiting for unfinished jobs
> > [  1%] Building CXX object
> > src/programs/CMakeFiles/view_objlib.dir/view/view.cpp.o
> > [  1%] Built target view_objlib
> > [  1%] Building C object
> > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/md.c.o
> > [  2%] Building C object
> > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/membed.c.o
> > [  2%] Building C object
> > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/pme_loadbal.c.o
> > [  2%] Building C object
> > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/repl_ex.c.o
> > [  2%] Building CXX object
> > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o
> > [  2%] Building C object
> > src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/runner.c.o
> > [  2%] Built target mdrun_objlib
> > Makefile:162: recipe for target 'all' failed
> > make: *** [all] Error 2
> >
> >
> > How to fix this error?
> >
> > Cmake version is 3.11.0
> > FFTW version is 3.3.7
> >
> > Thank you.
> > --
> > 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.
> >
> --
> 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.
-- 
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Re: [gmx-users] Installation error

2018-03-24 Thread Mark Abraham

Hi,

If you have fftw 3.3.7, then you don't need to ask the GROMACS build system
to download and build fftw for you. The error is suggesting that the issue
is that your CMake build wasn't configured to be able to do the download
that your asking GROMACS to ask CMake to do.

Mark

On Sat, Mar 24, 2018, 12:28 ali akgün  wrote:

> Hello,
>
> I got an error in gromacs-5.0.7 installiation cmake part.
>
> My error is:
>
>
> Scanning dependencies of target fftwBuild
> Scanning dependencies of target mdrun_objlib
> Scanning dependencies of target view_objlib
> [  0%] Performing pre-download step for 'fftwBuild'
> [  0%] Creating directories for 'fftwBuild'
> -- downloading...
>  src='http://www.fftw.org/fftw-3.3.3.tar.gz'
>
> dest='/home/ali/Downloads/gromacs-5.0.7/build/src/contrib/fftw/fftw.tar.gz'
> CMake Error at fftw-download.cmake:9 (file):
>   file DOWNLOAD not supported by bootstrap cmake.
>
>
> src/contrib/fftw/CMakeFiles/fftwBuild.dir/build.make:119: recipe for target
>
> 'src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/fftwBuild-pre-download'
> failed
> make[2]: ***
>
> [src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/fftwBuild-pre-download]
> Error 1
> make[2]: *** Waiting for unfinished jobs
> CMakeFiles/Makefile2:1124: recipe for target
> 'src/contrib/fftw/CMakeFiles/fftwBuild.dir/all' failed
> make[1]: *** [src/contrib/fftw/CMakeFiles/fftwBuild.dir/all] Error 2
> make[1]: *** Waiting for unfinished jobs
> [  1%] Building CXX object
> src/programs/CMakeFiles/view_objlib.dir/view/view.cpp.o
> [  1%] Built target view_objlib
> [  1%] Building C object
> src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/md.c.o
> [  2%] Building C object
> src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/membed.c.o
> [  2%] Building C object
> src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/pme_loadbal.c.o
> [  2%] Building C object
> src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/repl_ex.c.o
> [  2%] Building CXX object
> src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o
> [  2%] Building C object
> src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/runner.c.o
> [  2%] Built target mdrun_objlib
> Makefile:162: recipe for target 'all' failed
> make: *** [all] Error 2
>
>
> How to fix this error?
>
> Cmake version is 3.11.0
> FFTW version is 3.3.7
>
> Thank you.
> --
> 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.
>
-- 
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Re: [gmx-users] installation error

2018-03-21 Thread Mark Abraham

Hi,

Your CMake installation is broken. You should probably install it again,
depending how you did it last time.

Mark

On Wed, Mar 21, 2018, 16:39 ali akgün  wrote:

> Hello,
>
> I got an error in gromacs-5.1.5 installiation cmake part.
>
> My error is:
>
> *** glibc detected *** cmake: free(): invalid pointer: 0x009f241d
> ***
>
> How to fix this error?
>
> Thank you.
> --
> 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.
>
-- 
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Re: [gmx-users] installation error gromacs-imd

2016-06-09 Thread Andrian Saputra

Thanks Mark...
Pada tanggal 9 Jun 2016 18.58, "Mark Abraham" 
menulis:

> Hi,
>
> Please use a released version of GROMACS and don't smash your OS by running
> make with sudo. Then we can consider problems that may arise :-)
>
> Mark
>
> On Thu, 9 Jun 2016 11:30 Andrian Saputra  wrote:
>
> > Hi..May be its not a gromacs master..
> > But i think there is no problem with source
> > Pada tanggal 9 Jun 2016 15.48, "Kutzner, Carsten" 
> > menulis:
> >
> > >
> > > > On 09 Jun 2016, at 09:33, Andrian Saputra 
> > > wrote:
> > > >
> > > > Hi,,
> > > >
> > > > Ya i hve tried to install version 5.0 and all compilation is ok...
> but
> > i
> > > > familiar with version 4.5, 4.6... version 5.0 need some changes in
> mdp
> > > > file...
> > > But isn't this the master version of GROMACS that you tried to compile?
> > > For that version you will probably have to do some more adaptations of
> > > your .mdp file.
> > >
> > > There is no IMD for 4.5 and 4.6, you will need to use 5.0 or later.
> > >
> > > Carsten
> > >
> > > >
> > > > Do you have idea about the error ??
> > > >
> > > > Thank you
> > > > Pada tanggal 9 Jun 2016 14.16, "Kutzner, Carsten" 
> > > menulis:
> > > >
> > > >> Hi,
> > > >>
> > > >> the error message you see has nothing to do with IMD. Have you tried
> > > >> to install a Gromacs 5.0 or 5.1 or 2016 version? These should all
> > > >> work out of the box with IMD.
> > > >>
> > > >> Best,
> > > >>  Carsten
> > > >>
> > > >>
> > > >>> On 09 Jun 2016, at 04:35, Andrian Saputra 
> > > >> wrote:
> > > >>>
> > > >>> Dear gromacs users
> > > >>>
> > > >>> i was trying to install gromacs-imd that was developed by Martin
> > > Hoefling
> > > >>> http://www.mpibpc.mpg.de/grubmueller/interactivemd
> > > >>>
> > > >>> all configuration is ok with this command:
> > > >>>
> > > >>> CC=$HOME/software/openmpi/bin/mpicc
> > > >>> CXX=$HOME/software/openmpi/bin/mpicxx
> > > >>> F77=$HOME/software/openmpi/bin/mpif77
> > > >>> F90=$HOME/software/openmpi/bin/mpif90
> > > >>>
> > CMAKE_PREFIX_PATH=$HOME/software/fftw-3.3/build:$HOME/software/openmpi
> > > >>>
> > > >>
> > >
> >
> CMAKE_LIBRARY_PATH=$HOME/software/fftw-3.3/build/lib:$HOME/software/openmpi/lib
> > > >>>
> > > >>>
> > > >>
> > >
> >
> CMAKE_INCLUDE_PATH=$HOME/software/fftw-3.3/build/include:$HOME/software/openmpi/include
> > > >>>
> > > >>> cmake .. -DGMX_MPI=ON -DGMX_DOUBLE=ON
> > > >>> -DCMAKE_INSTALL_PREFIX=$HOME/software/gromacs
> -DGMX_INTERNAL_BOOST=ON
> > > >>> -DGMX_QMMM_PROGRAM=ORCA
> > > >>> -DFFTW_LIBRARY=$HOME/software/fftw-3.3/build/lib/libfftw3.a
> -Wno-dev
> > > >>>
> > > >>> after i execute sudo make -j4, i got this error message:
> > > >>>
> > > >>>
> > > >>
> > >
> >
> /home/pkimia/software/gromacs-master-imd/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/kernelutil_x86_avx_256_double.h:332:30:
> > > >>> error: incompatible type for argument 1 of ‘gmx_mm256_set_m128’
> > > >>>*z3 = gmx_mm256_set_m128(tz,tz);
> > > >>> .
> > > >>> .
> > > >>> .
> > > >>> .bla bla bla...
> > > >>> src/gromacs/CMakeFiles/libgromacs.dir/build.make:8774: recipe for
> > > target
> > > >>>
> > > >>
> > >
> >
> 'src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o'
> > > >>> failed
> > > >>> make[2]: ***
> > > >>>
> > > >>
> > >
> >
> [src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o]
> > > >>> Error 1
> > > >>> CMakeFiles/Makefile2:1586: recipe for target
> > > >>> 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
> > > >>> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> > > >>> Makefile:160: recipe for target 'all' failed
> > > >>> make: *** [all] Error 2
> > > >>>
> > > >>>
> > > >>> anyone can suggest me to solve this errro ? thank you so much
> > > >>> --
> > > >>> --
> > > >>> 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.
> > > >>
> > > >> --
> > > >> 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.
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > >

Re: [gmx-users] installation error gromacs-imd

2016-06-09 Thread Mark Abraham

Hi,

Please use a released version of GROMACS and don't smash your OS by running
make with sudo. Then we can consider problems that may arise :-)

Mark

On Thu, 9 Jun 2016 11:30 Andrian Saputra  wrote:

> Hi..May be its not a gromacs master..
> But i think there is no problem with source
> Pada tanggal 9 Jun 2016 15.48, "Kutzner, Carsten" 
> menulis:
>
> >
> > > On 09 Jun 2016, at 09:33, Andrian Saputra 
> > wrote:
> > >
> > > Hi,,
> > >
> > > Ya i hve tried to install version 5.0 and all compilation is ok... but
> i
> > > familiar with version 4.5, 4.6... version 5.0 need some changes in mdp
> > > file...
> > But isn't this the master version of GROMACS that you tried to compile?
> > For that version you will probably have to do some more adaptations of
> > your .mdp file.
> >
> > There is no IMD for 4.5 and 4.6, you will need to use 5.0 or later.
> >
> > Carsten
> >
> > >
> > > Do you have idea about the error ??
> > >
> > > Thank you
> > > Pada tanggal 9 Jun 2016 14.16, "Kutzner, Carsten" 
> > menulis:
> > >
> > >> Hi,
> > >>
> > >> the error message you see has nothing to do with IMD. Have you tried
> > >> to install a Gromacs 5.0 or 5.1 or 2016 version? These should all
> > >> work out of the box with IMD.
> > >>
> > >> Best,
> > >>  Carsten
> > >>
> > >>
> > >>> On 09 Jun 2016, at 04:35, Andrian Saputra 
> > >> wrote:
> > >>>
> > >>> Dear gromacs users
> > >>>
> > >>> i was trying to install gromacs-imd that was developed by Martin
> > Hoefling
> > >>> http://www.mpibpc.mpg.de/grubmueller/interactivemd
> > >>>
> > >>> all configuration is ok with this command:
> > >>>
> > >>> CC=$HOME/software/openmpi/bin/mpicc
> > >>> CXX=$HOME/software/openmpi/bin/mpicxx
> > >>> F77=$HOME/software/openmpi/bin/mpif77
> > >>> F90=$HOME/software/openmpi/bin/mpif90
> > >>>
> CMAKE_PREFIX_PATH=$HOME/software/fftw-3.3/build:$HOME/software/openmpi
> > >>>
> > >>
> >
> CMAKE_LIBRARY_PATH=$HOME/software/fftw-3.3/build/lib:$HOME/software/openmpi/lib
> > >>>
> > >>>
> > >>
> >
> CMAKE_INCLUDE_PATH=$HOME/software/fftw-3.3/build/include:$HOME/software/openmpi/include
> > >>>
> > >>> cmake .. -DGMX_MPI=ON -DGMX_DOUBLE=ON
> > >>> -DCMAKE_INSTALL_PREFIX=$HOME/software/gromacs -DGMX_INTERNAL_BOOST=ON
> > >>> -DGMX_QMMM_PROGRAM=ORCA
> > >>> -DFFTW_LIBRARY=$HOME/software/fftw-3.3/build/lib/libfftw3.a -Wno-dev
> > >>>
> > >>> after i execute sudo make -j4, i got this error message:
> > >>>
> > >>>
> > >>
> >
> /home/pkimia/software/gromacs-master-imd/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/kernelutil_x86_avx_256_double.h:332:30:
> > >>> error: incompatible type for argument 1 of ‘gmx_mm256_set_m128’
> > >>>*z3 = gmx_mm256_set_m128(tz,tz);
> > >>> .
> > >>> .
> > >>> .
> > >>> .bla bla bla...
> > >>> src/gromacs/CMakeFiles/libgromacs.dir/build.make:8774: recipe for
> > target
> > >>>
> > >>
> >
> 'src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o'
> > >>> failed
> > >>> make[2]: ***
> > >>>
> > >>
> >
> [src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o]
> > >>> Error 1
> > >>> CMakeFiles/Makefile2:1586: recipe for target
> > >>> 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
> > >>> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> > >>> Makefile:160: recipe for target 'all' failed
> > >>> make: *** [all] Error 2
> > >>>
> > >>>
> > >>> anyone can suggest me to solve this errro ? thank you so much
> > >>> --
> > >>> --
> > >>> 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.
> > >>
> > >> --
> > >> 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.
> > > --
> > > 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.
> >
> > --
> > Gromacs Users mailing

Re: [gmx-users] installation error gromacs-imd

2016-06-09 Thread Andrian Saputra

Hi..May be its not a gromacs master..
But i think there is no problem with source
Pada tanggal 9 Jun 2016 15.48, "Kutzner, Carsten"  menulis:

>
> > On 09 Jun 2016, at 09:33, Andrian Saputra 
> wrote:
> >
> > Hi,,
> >
> > Ya i hve tried to install version 5.0 and all compilation is ok... but i
> > familiar with version 4.5, 4.6... version 5.0 need some changes in mdp
> > file...
> But isn't this the master version of GROMACS that you tried to compile?
> For that version you will probably have to do some more adaptations of
> your .mdp file.
>
> There is no IMD for 4.5 and 4.6, you will need to use 5.0 or later.
>
> Carsten
>
> >
> > Do you have idea about the error ??
> >
> > Thank you
> > Pada tanggal 9 Jun 2016 14.16, "Kutzner, Carsten" 
> menulis:
> >
> >> Hi,
> >>
> >> the error message you see has nothing to do with IMD. Have you tried
> >> to install a Gromacs 5.0 or 5.1 or 2016 version? These should all
> >> work out of the box with IMD.
> >>
> >> Best,
> >>  Carsten
> >>
> >>
> >>> On 09 Jun 2016, at 04:35, Andrian Saputra 
> >> wrote:
> >>>
> >>> Dear gromacs users
> >>>
> >>> i was trying to install gromacs-imd that was developed by Martin
> Hoefling
> >>> http://www.mpibpc.mpg.de/grubmueller/interactivemd
> >>>
> >>> all configuration is ok with this command:
> >>>
> >>> CC=$HOME/software/openmpi/bin/mpicc
> >>> CXX=$HOME/software/openmpi/bin/mpicxx
> >>> F77=$HOME/software/openmpi/bin/mpif77
> >>> F90=$HOME/software/openmpi/bin/mpif90
> >>> CMAKE_PREFIX_PATH=$HOME/software/fftw-3.3/build:$HOME/software/openmpi
> >>>
> >>
> CMAKE_LIBRARY_PATH=$HOME/software/fftw-3.3/build/lib:$HOME/software/openmpi/lib
> >>>
> >>>
> >>
> CMAKE_INCLUDE_PATH=$HOME/software/fftw-3.3/build/include:$HOME/software/openmpi/include
> >>>
> >>> cmake .. -DGMX_MPI=ON -DGMX_DOUBLE=ON
> >>> -DCMAKE_INSTALL_PREFIX=$HOME/software/gromacs -DGMX_INTERNAL_BOOST=ON
> >>> -DGMX_QMMM_PROGRAM=ORCA
> >>> -DFFTW_LIBRARY=$HOME/software/fftw-3.3/build/lib/libfftw3.a -Wno-dev
> >>>
> >>> after i execute sudo make -j4, i got this error message:
> >>>
> >>>
> >>
> /home/pkimia/software/gromacs-master-imd/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/kernelutil_x86_avx_256_double.h:332:30:
> >>> error: incompatible type for argument 1 of ‘gmx_mm256_set_m128’
> >>>*z3 = gmx_mm256_set_m128(tz,tz);
> >>> .
> >>> .
> >>> .
> >>> .bla bla bla...
> >>> src/gromacs/CMakeFiles/libgromacs.dir/build.make:8774: recipe for
> target
> >>>
> >>
> 'src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o'
> >>> failed
> >>> make[2]: ***
> >>>
> >>
> [src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o]
> >>> Error 1
> >>> CMakeFiles/Makefile2:1586: recipe for target
> >>> 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
> >>> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> >>> Makefile:160: recipe for target 'all' failed
> >>> make: *** [all] Error 2
> >>>
> >>>
> >>> anyone can suggest me to solve this errro ? thank you so much
> >>> --
> >>> --
> >>> 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.
> >>
> >> --
> >> 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.
> > --
> > 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.
>
> --
> 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.
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* Can't post? Read

Re: [gmx-users] installation error gromacs-imd

2016-06-09 Thread Kutzner, Carsten


> On 09 Jun 2016, at 09:33, Andrian Saputra  wrote:
> 
> Hi,,
> 
> Ya i hve tried to install version 5.0 and all compilation is ok... but i
> familiar with version 4.5, 4.6... version 5.0 need some changes in mdp
> file...
But isn't this the master version of GROMACS that you tried to compile?
For that version you will probably have to do some more adaptations of
your .mdp file.

There is no IMD for 4.5 and 4.6, you will need to use 5.0 or later.

Carsten

> 
> Do you have idea about the error ??
> 
> Thank you
> Pada tanggal 9 Jun 2016 14.16, "Kutzner, Carsten"  menulis:
> 
>> Hi,
>> 
>> the error message you see has nothing to do with IMD. Have you tried
>> to install a Gromacs 5.0 or 5.1 or 2016 version? These should all
>> work out of the box with IMD.
>> 
>> Best,
>>  Carsten
>> 
>> 
>>> On 09 Jun 2016, at 04:35, Andrian Saputra 
>> wrote:
>>> 
>>> Dear gromacs users
>>> 
>>> i was trying to install gromacs-imd that was developed by Martin Hoefling
>>> http://www.mpibpc.mpg.de/grubmueller/interactivemd
>>> 
>>> all configuration is ok with this command:
>>> 
>>> CC=$HOME/software/openmpi/bin/mpicc
>>> CXX=$HOME/software/openmpi/bin/mpicxx
>>> F77=$HOME/software/openmpi/bin/mpif77
>>> F90=$HOME/software/openmpi/bin/mpif90
>>> CMAKE_PREFIX_PATH=$HOME/software/fftw-3.3/build:$HOME/software/openmpi
>>> 
>> CMAKE_LIBRARY_PATH=$HOME/software/fftw-3.3/build/lib:$HOME/software/openmpi/lib
>>> 
>>> 
>> CMAKE_INCLUDE_PATH=$HOME/software/fftw-3.3/build/include:$HOME/software/openmpi/include
>>> 
>>> cmake .. -DGMX_MPI=ON -DGMX_DOUBLE=ON
>>> -DCMAKE_INSTALL_PREFIX=$HOME/software/gromacs -DGMX_INTERNAL_BOOST=ON
>>> -DGMX_QMMM_PROGRAM=ORCA
>>> -DFFTW_LIBRARY=$HOME/software/fftw-3.3/build/lib/libfftw3.a -Wno-dev
>>> 
>>> after i execute sudo make -j4, i got this error message:
>>> 
>>> 
>> /home/pkimia/software/gromacs-master-imd/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/kernelutil_x86_avx_256_double.h:332:30:
>>> error: incompatible type for argument 1 of ‘gmx_mm256_set_m128’
>>>*z3 = gmx_mm256_set_m128(tz,tz);
>>> .
>>> .
>>> .
>>> .bla bla bla...
>>> src/gromacs/CMakeFiles/libgromacs.dir/build.make:8774: recipe for target
>>> 
>> 'src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o'
>>> failed
>>> make[2]: ***
>>> 
>> [src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o]
>>> Error 1
>>> CMakeFiles/Makefile2:1586: recipe for target
>>> 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
>>> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
>>> Makefile:160: recipe for target 'all' failed
>>> make: *** [all] Error 2
>>> 
>>> 
>>> anyone can suggest me to solve this errro ? thank you so much
>>> --
>>> --
>>> 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.
>> 
>> --
>> 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.
> -- 
> 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.

-- 
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* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] installation error gromacs-imd

2016-06-09 Thread Andrian Saputra

Hi,,

Ya i hve tried to install version 5.0 and all compilation is ok... but i
familiar with version 4.5, 4.6... version 5.0 need some changes in mdp
file...

Do you have idea about the error ??

Thank you
Pada tanggal 9 Jun 2016 14.16, "Kutzner, Carsten"  menulis:

> Hi,
>
> the error message you see has nothing to do with IMD. Have you tried
> to install a Gromacs 5.0 or 5.1 or 2016 version? These should all
> work out of the box with IMD.
>
> Best,
>   Carsten
>
>
> > On 09 Jun 2016, at 04:35, Andrian Saputra 
> wrote:
> >
> > Dear gromacs users
> >
> > i was trying to install gromacs-imd that was developed by Martin Hoefling
> > http://www.mpibpc.mpg.de/grubmueller/interactivemd
> >
> > all configuration is ok with this command:
> >
> > CC=$HOME/software/openmpi/bin/mpicc
> > CXX=$HOME/software/openmpi/bin/mpicxx
> > F77=$HOME/software/openmpi/bin/mpif77
> > F90=$HOME/software/openmpi/bin/mpif90
> > CMAKE_PREFIX_PATH=$HOME/software/fftw-3.3/build:$HOME/software/openmpi
> >
> CMAKE_LIBRARY_PATH=$HOME/software/fftw-3.3/build/lib:$HOME/software/openmpi/lib
> >
> >
> CMAKE_INCLUDE_PATH=$HOME/software/fftw-3.3/build/include:$HOME/software/openmpi/include
> >
> > cmake .. -DGMX_MPI=ON -DGMX_DOUBLE=ON
> > -DCMAKE_INSTALL_PREFIX=$HOME/software/gromacs -DGMX_INTERNAL_BOOST=ON
> > -DGMX_QMMM_PROGRAM=ORCA
> > -DFFTW_LIBRARY=$HOME/software/fftw-3.3/build/lib/libfftw3.a -Wno-dev
> >
> > after i execute sudo make -j4, i got this error message:
> >
> >
> /home/pkimia/software/gromacs-master-imd/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/kernelutil_x86_avx_256_double.h:332:30:
> > error: incompatible type for argument 1 of ‘gmx_mm256_set_m128’
> > *z3 = gmx_mm256_set_m128(tz,tz);
> > .
> > .
> > .
> > .bla bla bla...
> > src/gromacs/CMakeFiles/libgromacs.dir/build.make:8774: recipe for target
> >
> 'src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o'
> > failed
> > make[2]: ***
> >
> [src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o]
> > Error 1
> > CMakeFiles/Makefile2:1586: recipe for target
> > 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
> > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> > Makefile:160: recipe for target 'all' failed
> > make: *** [all] Error 2
> >
> >
> > anyone can suggest me to solve this errro ? thank you so much
> > --
> > --
> > 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.
>
> --
> 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.
-- 
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* 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
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] installation error gromacs-imd

2016-06-09 Thread Kutzner, Carsten

Hi,

the error message you see has nothing to do with IMD. Have you tried
to install a Gromacs 5.0 or 5.1 or 2016 version? These should all
work out of the box with IMD.

Best,
  Carsten


> On 09 Jun 2016, at 04:35, Andrian Saputra  wrote:
> 
> Dear gromacs users
> 
> i was trying to install gromacs-imd that was developed by Martin Hoefling
> http://www.mpibpc.mpg.de/grubmueller/interactivemd
> 
> all configuration is ok with this command:
> 
> CC=$HOME/software/openmpi/bin/mpicc
> CXX=$HOME/software/openmpi/bin/mpicxx
> F77=$HOME/software/openmpi/bin/mpif77
> F90=$HOME/software/openmpi/bin/mpif90
> CMAKE_PREFIX_PATH=$HOME/software/fftw-3.3/build:$HOME/software/openmpi
> CMAKE_LIBRARY_PATH=$HOME/software/fftw-3.3/build/lib:$HOME/software/openmpi/lib
> 
> CMAKE_INCLUDE_PATH=$HOME/software/fftw-3.3/build/include:$HOME/software/openmpi/include
> 
> cmake .. -DGMX_MPI=ON -DGMX_DOUBLE=ON
> -DCMAKE_INSTALL_PREFIX=$HOME/software/gromacs -DGMX_INTERNAL_BOOST=ON
> -DGMX_QMMM_PROGRAM=ORCA
> -DFFTW_LIBRARY=$HOME/software/fftw-3.3/build/lib/libfftw3.a -Wno-dev
> 
> after i execute sudo make -j4, i got this error message:
> 
> /home/pkimia/software/gromacs-master-imd/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/kernelutil_x86_avx_256_double.h:332:30:
> error: incompatible type for argument 1 of ‘gmx_mm256_set_m128’
> *z3 = gmx_mm256_set_m128(tz,tz);
> .
> .
> .
> .bla bla bla...
> src/gromacs/CMakeFiles/libgromacs.dir/build.make:8774: recipe for target
> 'src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o'
> failed
> make[2]: ***
> [src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecRF_VdwNone_GeomW3W3_avx_256_double.c.o]
> Error 1
> CMakeFiles/Makefile2:1586: recipe for target
> 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> Makefile:160: recipe for target 'all' failed
> make: *** [all] Error 2
> 
> 
> anyone can suggest me to solve this errro ? thank you so much
> --
> -- 
> 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.

-- 
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Re: [gmx-users] Installation Error

2015-04-11 Thread Justin Lemkul




On 4/11/15 9:19 AM, su wrote:

Dear All I am trying to install Gromacs on ubuntu. I have followed the quick
and dirty tutorial but when i untar the gromacs-4.6.4.tar.gz file it gives
error that no such file ir directory. File is located in the system , i
dont know why it is happening. please help


If it were in the working directory, the error wouldn't come up.  This is simply 
an issue with file management.  The file is not where you think it is or want it 
to be.


I recommend installing the current version rather than something outdated.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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