[gmx-users] gromacs.org_gmx-users Digest, Vol 119, Issue 8

[sauravsaha]

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Today's Topics:

   1. Regarding structure analysis of DNA (Sathish Kumar)
   2. Set the environment variables of "FFTW3_INCLUDE_DIR"	and
      "FFTW3_LIBRARIES" (Hassan Aaryapour)


----------------------------------------------------------------------

Message: 1
Date: Mon, 3 Mar 2014 01:05:41 -0800
From: Sathish Kumar <sathishk238 at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Subject: [gmx-users] Regarding structure analysis of DNA
Message-ID:
	<CAFi=hWK79KpmzOy9NCEkO+Qf+9xuMMUztWoYa8pmRAGbNhbcAQ at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hai
          I have done simulation of DNA on carbon nano tube surface. I want
to calculate structural changes (means changes in stacking, puckering
angles and bending of helix) in DNA. Can any suggest me how to calculate
these things.

 Thank You Very Much.

regards
M.SathishKumar


------------------------------

Message: 2
Date: Mon, 3 Mar 2014 13:56:01 +0330
From: Hassan Aaryapour <hassan.gromacs at gmail.com>
To: "gromacs.org_gmx-users"
	<gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] Set the environment variables of
	"FFTW3_INCLUDE_DIR"	and "FFTW3_LIBRARIES"
Message-ID:
	<CACqAq9-NSM-eXTkCPwYR6KHR1+0T75x4nw0mBrunLXHc_ehMiQ at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Dear Gmx-user;
I want to install double precision gromacs 4.5.3 and FFTW 3.3.2 in my
home directory.
first, according to the FFTW installation instructions I installed and
introduced it to bash shell it as the following order:

$tar -xzvf fftw-3.3.2.tar.gz
$./configure --enable-threads --prefix=/home/WeNMR/ProgramFiles/fftw
$make
$make install

export CPPFLAGS=-I/home/WeNMR/ProgramFiles/fftw/include
export LDFLAGS=-L/home/WeNMR/ProgramFiles/fftw/lib

but it isn't found automatically by cmake when I want to install gromacs.
and this error was appeared:

 CMake Error at
/usr/local/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:108
(message):
   Could not find FFTW3.  Provide the fftw3 install directory in the
   FFTW3_ROOT_DIR environment variable.  (missing: FFTW3_LIBRARIES
   FFTW3_INCLUDE_DIR)
 Call Stack (most recent call first):
   /usr/local/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:315
(_FPHSA_FAILURE_MESSAGE)
   cmake/FindFFTW3.cmake:31 (find_package_handle_standard_args)
   CMakeLists.txt:636 (find_package)


How can I set the environment variables for "FFTW3_INCLUDE_DIR" and
"FFTW3_LIBRARIES"?
can I add my FFTW installed path to "CMakeLists.txt" file in the
related section in below? how?

if(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
#    MESSAGE(STATUS "Using external FFT library - fftw3")
    if(GMX_DOUBLE)
        find_package(FFTW3 REQUIRED)
		include_directories(${FFTW3_INCLUDE_DIR})
        set(FFT_LIBRARIES ${FFTW3_LIBRARIES})
        set(PKG_FFT "fftw3")
    else(GMX_DOUBLE)
        find_package(FFTW3F REQUIRED)
        include_directories(${FFTW3F_INCLUDE_DIR})
        set(FFT_LIBRARIES ${FFTW3F_LIBRARIES})
        set(PKG_FFT "fftw3f")
    endif(GMX_DOUBLE)


Thank you in advance
Hassan


------------------------------

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End of gromacs.org_gmx-users Digest, Vol 119, Issue 8
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