[gmx-users] Version problem

Mark Abraham mark.j.abraham at gmail.com
Thu Nov 6 13:25:01 CET 2014 

Hi,

Well, you need to find out where you installed it (default /usr/local/bin).
Using "which" or "locate" will only find the version from your OS
distribution. Since you plan to use 5.0.2, you should uninstall the OS
version using the package manager, to save yourself from further accidental
confusion.

Mark

On Thu, Nov 6, 2014 at 12:43 PM, <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!
> >> >>
> >> >> * 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-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
> >> >
> >> > --
> >> > 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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> >> >
> >> > * For (un)subscribe requests visit
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> >> send
> >> > a mail to gmx-users-request at gromacs.org.
> >> >
> >> > --
> >> > This message has been scanned for viruses and
> >> > dangerous content by MailScanner, and is
> >> > believed to be clean.
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >> 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!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
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> >> send a mail to gmx-users-request at gromacs.org.
> >>
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
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> > posting!
> >
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> >
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> send
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> >
> > --
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> > believed to be clean.
> >
> >
>
>
>
> --
> 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!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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