[gmx-users] Version problem

Thu Nov 6 23:03:34 CET 2014

can look for all files with name mdrun by

$ find / -name mdrun * > mdrun_search
and then
$ cat mdrun_search

On Thu, Nov 6, 2014 at 7:25 AM, Erik Marklund <erik.marklund at chem.ox.ac.uk>
wrote:

> Hi,
>
> 'which mdrun' only tells you the location of the mdrun you're currently
> using and is no good here. How did you install 5.0.2? The CMake files
> should tell you where installation directory is.
>
> Kind regards,
> Erik
>
> On 6 Nov 2014, at 11:43, satya at physics.iisc.ernet.in wrote:
>
> >
> > tried "which mdrun"
> > showing the path /usr/bin/mdrun, which v4.6.5, however I have downloaded
> > v5.0.2.tar.gz and used for installation.
> >
> >
> >> try to find mdrun program by typing this command on terminal:
> >> "which mdrun"
> >> will show path of mdrun program where it located.
> >> On Nov 6, 2014 4:01 PM, <satya at physics.iisc.ernet.in> wrote:
> >>
> >>> Dear Dr. Carsten Kutzner,
> >>>      I am unable to find the "gmx5/bin/GMXRC" in my machine,
> >>> used 'locate' and 'find' to search the location.
> >>> However I have source the following:
> >>> source /usr/share/gromacs/shell-specific/GMXRC.bashrc
> >>> Without this also mdrun is running. I am definitely missing something.
> >>> Kindly help.
> >>>
> >>> With best regards,
> >>>
> >>> Satya
> >>>
> >>>> On 06 Nov 2014, at 07:15, satya at physics.iisc.ernet.in wrote:
> >>>>
> >>>>> Dear all,
> >>>>> I am new to GROMACS, just finish installation of v5.0.2, started
> >>> reading
> >>>>> online manual, as instructed executed the command: mdrun -version and
> >>>>> the
> >>>>> printout pasted below.
> >>>>>
> >>>>> It is printing GROMACS version 4.6.5, however I have installed
> >>> version
> >>>>> 5.0.2. What is the problem?
> >>>> Find the directory to where you have installed your GROMACS 5.0
> >>>> executables
> >>>> and then do
> >>>>
> >>>> source /path/to/gmx5/bin/GMXRC
> >>>>
> >>>> which mdrun
> >>>>
> >>>> should now give you the 5.0 mdrun
> >>>>
> >>>> Carsten
> >>>>
> >>>>>
> >>>>> Regards,
> >>>>> Satyabrata Das
> >>>>>
> >>>>>
> ======================================================================
> >>>>> Program: mdrun
> >>>>> Gromacs version:    VERSION 4.6.5
> >>>>> Precision:          single
> >>>>> Memory model:       64 bit
> >>>>> MPI library:        thread_mpi
> >>>>> OpenMP support:     enabled
> >>>>> GPU support:        disabled
> >>>>> invsqrt routine:    gmx_software_invsqrt(x)
> >>>>> CPU acceleration:   SSE4.1
> >>>>> FFT library:        fftw-3.3.3-sse2-avx
> >>>>> Large file support: enabled
> >>>>> RDTSCP usage:       enabled
> >>>>> Built on:           Sun Dec 15 04:01:11 UTC 2013
> >>>>> Built by:           buildd at panlong [CMAKE]
> >>>>> Build OS/arch:      Linux 3.2.0-37-generic x86_64
> >>>>> Build CPU vendor:   GenuineIntel
> >>>>> Build CPU brand:    Intel(R) Xeon(R) CPU           E5620  @ 2.40GHz
> >>>>> Build CPU family:   6   Model: 44   Stepping: 2
> >>>>> Build CPU features: aes apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr
> >>>>> nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3
> >>>>> sse4.1
> >>>>> sse4.2 ssse3
> >>>>> C compiler:         /usr/bin/x86_64-linux-gnu-gcc GNU gcc-4.8.real
> >>>>> (Ubuntu/Linaro 4.8.2-10ubuntu1) 4.8.2
> >>>>> C compiler flags:   -msse4.1    -Wextra
> >>> -Wno-missing-field-initializers
> >>>>> -Wno-sign-compare -Wall -Wno-unused -Wunused-value
> >>> -Wno-unused-parameter
> >>>>> -Wno-array-bounds -Wno-maybe-uninitialized -Wno-strict-overflow
> >>>>> -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -O3
> >>>>> -DNDEBUG
> >>>>> satyabrata at satyabrata-desktop:~$
> >>>>>
> >>>>>
> >>>>>
> >>>>> --
> >>>>> This message has been scanned for viruses and
> >>>>> dangerous content by MailScanner, and is
> >>>>> believed to be clean.
> >>>>>
> >>>>> --
> >>>>> Gromacs Users mailing list
> >>>>>
> >>>>> * Please search the archive at
> >>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >>>>> posting!
> >>>>>
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> or
> >>>>> send a mail to gmx-users-request at gromacs.org.
> >>>>
> >>>>
> >>>> --
> >>>> Dr. Carsten Kutzner
> >>>> Max Planck Institute for Biophysical Chemistry
> >>>> Theoretical and Computational Biophysics
> >>>> Am Fassberg 11, 37077 Goettingen, Germany
> >>>> Tel. +49-551-2012313, Fax: +49-551-2012302
> >>>> http://www.mpibpc.mpg.de/grubmueller/kutzner
> >>>> http://www.mpibpc.mpg.de/grubmueller/sppexa
> >>>>
> >>>> --
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> >>>>
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> >>>>
> >>>>
> >>>
> >>>
> >>>
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> >>
> >>
> >
> >
> >
> > --
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> > believed to be clean.
> >
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> >
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>