hoge
Gromacs/Amber Installation Guide for Winmostar V8 (Windows)

 1. Overview

Gromacs and sander launched from Winmostar are supposed to be compiled and installed with Cygwin.
To use Acpype[1] to make topology files, Acpype is required to be installed with cygwin.
Therefore, you need the packeges below to use all functions of Gromacs and sander on Winmostar.

  Cygwin
  Gromacs
  AmberTools14[2]
  Acpype
  ERmod

These softwares are distributed under GNU GPL, so they are available for free.

In addition MODYLAS and OpenMX installation are also described.
Theses programs are confirmed to run on Windows 10.
Please understand that calculation results are not guaranteed.

 2. Installation of each packege


 2-1. Cygwin


Download setup-x86.exe from http://www.cygwin.com/.
※The latest version is 2.881. (5 Sep 2017)
Follow the wizard of setup.exe and install it.
The packages which need to be installed are "All default" and the following packages.

  Archive - libbz2-devel
  Archive - unzip
  Devel - autoconf
  Devel - cmake
  Devel - flex
  Devel - gcc-fortran
  Devel - gcc-g++
  Devel - make
  Devel - pkg-config
  Devel - subversion
  Graphics - gnuplot
  Graphics - ImageMagick
  Interpreters - m4
  Interpreters - python2
  Libs - libboost-devel
  Libs - libfftw3-devel
  Libs - libmpfr4
  Libs - libnetcdf-devel
  Libs - libopenmpi-devel
  Libs - openmpi
  Math - bc
  Math - grace
  Math - liblapack-devel
  Net - openssh
  Python - python2-numpy
  Science - openbabel
  Shells - tcsh
  Utils - dos2unix
  Utils - patchutils


Package: _/libfontconfig-common
fontconfig_dtd.sh exit code 2

Above message might be shown after installation.
igore it and continue for now.
We recomment to edit /etc/profile.d/lang.sh so that
export LANG=C

 2-2. Gromacs


Download gromacs-5.0.7.tar.gz from http://www.gromacs.org/Downloads.
※ 5.1 or later have a problem for gmx rdf. So use 5.0.7 instead.
Launch cygwin terminal and compile as follows. (Set -DGMX_SIMD=AVX_256 for cmake to enable AVX.)

$ tar xvfz gromacs-5.0.7.tar.gz
$ cd gromacs-5.0.4
$ mkdir build
$ cd build
$ cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=OFF -DGMX_SIMD=SSE2 -DGMX_DOUBLE=OFF -DGMX_USE_RDTSCP=OFF
$ make
$ make install
$ cd ..
$ mkdir build_d
$ cd build_d
$ cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=OFF -DGMX_SIMD=SSE2 -DGMX_DOUBLE=ON -DGMX_USE_RDTSCP=OFF
$ make
$ make install

It is installed in /usr/local/gromacs.

Add
source /usr/local/gromacs/bin/GMXRC
to /etc/profile.d/winmostar.sh

 2-3. AmberTools14


Download AmberTools14.tar.bz2 from http://ambermd.org/AmberTools14-get.html.
Complie it as follows.

$ tar xvfj AmberTools14.tar.bz2
$ export AMBERHOME=~/amber14
$ cd $AMBERHOME
$ ./configure -cygwin -noX11 gnu
$ make install

※ In the case that compiling StringRoutines.cpp fails.
Add the following line on the head of AmberTools/src/cpptraj/src/StringRoutines.cpp
#define _GNU_SOURCE


$ cd ..
$ mv amber14 /usr/local

Add
export AMBERHOME=/usr/local/amber12
export PATH=$PATH:$AMBERHOME/bin
to /etc/profile.d/winmostar.sh

 2-4. Acpype


Get Acpype as follows.

$ svn checkout http://svn.code.sf.net/p/ccpn/code/branches/stable/ccpn/python/acpype/ acpype -r 8810
"/usr/bin/env python" failes when current directory is under C:\cygwin_wm .
$ vi acpype/acpype.py
#!/usr/bin/env python

#!/usr/bin/python

$ mv acpype /usr/local

Add
export PATH=$PATH:/usr/local/acpype
to /etc/profile.d/winmostar.sh

 2-5. ERmod


Download ermod-0.3.4.tar.gz from http://sourceforge.net/projects/ermod/files/?source=navbar
Compile as follows.

$ tar zxvf ermod-0.3.4.tar.gz
$ cd ermod-0.3.4/vmdplugins
$ make
$ cp compile/*.so libexec/
$ cd ..
$ ./configure --prefix=/usr/local/ermod --disable-mpi --enable-openmp
$ export LANG=C
$ make
$ make install

See ERmod wiki page for details.

 2-6. MODYLAS


You need agreement to MODYLAS License to use MODYLAS.

Get MODYLAS_1.0.4.tar_1.gz from http://www.modylas.org/.
Compile as follows.

$ tar -zxvf MODYLAS_1.0.4.tar_1.gz
$ cd MODYLAS_1.0.4/source
$ vi configure
Delete comments of COMDEFS and replace "-openmp -parallel -fpp" to "-cpp".
$ ./configure --with-kind-fortran-compiler=INTEL --prefix=/usr/local/MODYLAS_1.0.4
$ cd src
$ vi parse_f.f
Replace line 363
9000 format(‘ERROR:…’, i)
to
9000 format(‘ERROR:…’, i8)

$ make $ make install
Add
export PATH=$PATH:/usr/local/MODYLAS_1.0.4/bin
to /etc/profile.d/winmostar.sh

MODYLAS website for details.

You need other programs to use full function of MODYLAS.
Please contact Winmostar support.

 2-7. OpenMX


Get openmx3.8(openmx3.8.tar.gz) and patxh(patch3.8.3.tar.gz on 08/Mar./2017) from http://www.openmx-square.org/download.html.

Compile as follows.

$ tar xvfz openmx3.8.tar.gz
$ cd openmx3.8/source
$ cp ../../patch3.8.3.tar.gz .
$ tar xvfz patch3.8.3.tar.gz
$ vi makefile
Change CC, FC, CPPFLAGS, LIB as follows.
CC=gcc -fopenmp -O3 -I/usr/include -Dkcomp -Dnosse
FC=gfortran -O3 -I/usr/include -Dkcomp
CPPFLAGS=-DNDEBUG
LIB=-static /usr/lib/libfftw3.dll.a -llapack -lblas -lgfortran /usr/lib/libmpi_mpifh.dll.a /usr/lib/libmpi.dll.a -lquadmath

$ vi openmx_common.h
#define fp_bsize 200000

$ make
$ make install
$ gcc bandgnu13.c -lm -o ../work/bandgnu13.exe
$ make DosMain
$ cp -r ../../openmx3.8 /usr/local

Get fermisurfer_1.7.1.zip from https://ja.osdn.net/projects/fermisurfer/releases/
Unpack and install as follows.
$ unzip fermisurfer_1.7.1.zip
$ cp -r fermisurfer /usr/local/

Add
export PATH=$PATH:/usr/local/openmx3.8/work:/usr/local/fermisurfer/bin
export OPENMX_DATA_PATH=/usr/local/openmx3.8/DFT_DATA13
to /etc/profile.d/winmostar.sh

See OpenMX website and FermiSurfer website for details.

 3. Citation

1. SOUSA DA SILVA, A. W. & VRANKEN, W. F. ACPYPE - AnteChamber PYthon Parser interfacE.
BMC Research Notes 2012, 5:367 doi:10.1186/1756-0500-5-367 http://www.biomedcentral.com/1756-0500/5/367

2. Antechamber
J. Wang, W. Wang, P.A. Kollman and D.A. Case. "Automatic atom type and bond type perception in molecular mechanical calculations".
Journal of Molecular Graphics and Modelling, 25, 247-260 (2006).
J. Wang, R.M. Wolf, J.W. Caldwell, P.A. Kollman and D.A. Case. "Development and testing of a general AMBER force field".
Journal of Computational Chemistry, 25, 1157-1174 (2004).



©2008-2017 X-Ability. Co. Ltd.,