[gmx-users] Version problem

Thu Nov 6 13:12:53 CET 2014

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:~$
>> >>
>> >>
>> >>
>> >> --
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>> >> believed to be clean.
>> >>
>> >> --
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>> >>
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>> >
>> >
>> > --
>> > 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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This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.