''' !!! WORK IN PROGRESS    !!! '''\\
Last Update 04.2017, Authors: Jens Henrik Göbbert, ...

= VMD - Visual Molecular Dynamics
[[PageOutline]]


'''VMD''' is free, open-source software for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc.

* VMD may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure.
* VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others.
* VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation.
* VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.

* [http://www.ks.uiuc.edu/Research/vmd/ VMD (Visual Molecular Dynamics)]


== Prebuild on JURECA ==

VMD is prebuild on JURECA. \\
Please use the graphical login to JURECA ([wiki:vnc3d more infos]) to use VMD.

* You can find a VMD icon on the [wiki:vnc3d/strudel VNC Remote Desktop].\\
* Alternatively run {{{module spider VMD}}} on JURECA to check how to load the VMD module.

== Build ==

If you still want to build your own VMD:
* General build instructions can be found here:
  * http://www.ks.uiuc.edu/Research/vmd/doxygen/compiling.html#compiling
  * http://www.ks.uiuc.edu/Research/vmd/doxygen/configure.html#configure

All library and include paths are defined inside VMD's configure script (this is __no__ autoconf configure, but a VMD specific perl script).\\
The configure script creates a Makefile in the src directory.\\
This generated Makefile has to be to compile a VMD executable from the source code.\\

You find the needed modifications of the configure script for JURECA [attachment:vmd-1.9.3_configure.patch HERE].

* VMD was build on JURECA using !EasyBuild similar to the following script:
{{{ #!sh
#!/bin/sh

VMD_VERSION=1.9.3

module --force purge

# create pv_compile
mkdir -p vmd_compile/
cd vmd_compile

if true; then # disable/enable unpack+patch
  # unpack source
  cp ../vmd-${VMD_VERSION}.src.tar.gz .
  tar -xzf vmd-${VMD_VERSION}.src.tar.gz

  # patch VMD
  cp ../vmd-1.9.3_configure.patch .
  patch vmd-1.9.3/configure -i vmd-1.9.3_configure.patch
fi

# load environment
BUILDDIR=$(pwd)
INSTALLDIR=$(pwd)/install

module load Stages/Devel-2017a
module load GCCcore/.5.4.0
module load Intel
module load ParaStationMPI
module load CUDA

module load X11/20170129
module load Tk/.8.6.6
module load FLTK/.1.3.4
module load libGLU/.9.0.0

module load libpng/.1.6.28
module load zlib/.1.2.11

module load OSPRay/1.2.1
module load tbb/2017.4.174

module load OptiX/4.0.2

module load nvidia/.driver

########## BUILD PLUGINS 

# for vtfplugin, webpdbplugin
module load Tcl/.8.6.6
export TCLINC=-I$EBROOTTCL/include
export TCLLIB=-L$EBROOTTCL/lib
export TCLLDFLAGS=-ltcl

# for reading/writing NetCDF format files
module load netCDF/4.4.1.1
export NETCDFINC=-I$EBROOTNETCDF/include
export NETCDFLIB=-L$EBROOTNETCDF/lib 
export NETCDFLDFLAGS=-lnetcdf

# for hoomd plugin
module load expat/.2.2.0
export EXPATINC=-I$EBROOTEXPAT/include
export EXPATLIB=-L$EBROOTEXPAT/lib64
export EXPATLDFLAGS=-lexpat

# build plugins
mkdir -p $BUILDDIR/vmd-$VMD_VERSION/plugins
export PLUGINDIR=$BUILDDIR/vmd-$VMD_VERSION/plugins

if true; then # disable/enable build plugins
  cd $BUILDDIR/plugins
  make clean
  make LINUXAMD64 TCLINC=$TCLINC TCLLIB=$TCLLIB NETCDFINC=$NETCDFINC NETCDFLIB=$NETCDFLIB EXPATINC=$EXPATINC EXPATLIB=$EXPATLIB
  make distrib
fi

########## BUILD 3RD PARTY
# http://www.ks.uiuc.edu/Research/vmd/doxygen/extprogs.html
if true; then # disable/enable 3rd party

  # build surf
  cd $BUILDDIR/vmd-$VMD_VERSION/lib/surf
  tar -xzf surf.tar.Z 
  sed -i '/^# DO NOT DELETE THIS LINE/,+100 s/^/#/' Makefile
  make

  # build stride
  cd $BUILDDIR/vmd-$VMD_VERSION/lib/stride
  wget ftp://ftp.ebi.ac.uk/pub/software/unix/stride/src/stride.tar.gz
  tar -xzf stride.tar.gz
  sed -i 's/^#define MAX_AT_IN_RES.*/#define MAX_AT_IN_RES 75/' stride.h
  sed -i 's/^  return(SUCCESS);.*/  return(0);/' stride.c
  make

  # build tachyon
  cd $BUILDDIR/vmd-$VMD_VERSION/lib/tachyon
  wget http://jedi.ks.uiuc.edu/~johns/raytracer/files/0.99b6/tachyon-0.99b6.tar.gz
  tar -xzf tachyon-0.99b6.tar.gz
  cd tachyon/unix
  sed -i 's#^LINUX_GLX_INCS.*#LINUX_GLX_INCS = -I$(EBROOTX11)/include#' Make-opengl
  sed -i 's#^LINUX_GLX_LIBS.*#LINUX_GLX_LIBS = -L$(EBROOTX11)/lib -L$(NVIDIALIBDIR) -lGL -lX11#' Make-opengl
  make linux-64-thr-ogl
  cd $BUILDDIR/vmd-$VMD_VERSION/lib/tachyon
  mkdir lib_LINUXAMD64
  cp tachyon/compile/linux-64-thr-ogl/libtachyon.a lib_LINUXAMD64/
  mkdir include
  cp tachyon/src/*.h include/

fi

########## BUILD VMD
export VMDINSTALLBINDIR=$INSTALLDIR/bin
export VMDINSTALLLIBRARYDIR=$INSTALLDIR/lib

# For python support
module load Python/2.7.13
export PYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python2.7
export PYTHON_LIBRARY_DIR=$EBROOTPYTHON/lib/python2.7

module load SciPy-Stack/2017a-Python-2.7.13
export NUMPY_INCLUDE_DIR=$EBROOTSCIPYMINSTACK/lib/python2.7/site-packages/numpy-1.12.0-py2.7-linux-x86_64.egg/numpy/core/include
export NUMPY_LIBRARY_DIR=$EBROOTSCIPYMINSTACK/lib/python2.7/site-packages/numpy-1.12.0-py2.7-linux-x86_64.egg/numpy/core/lib

# For tcl support, yes, in addition to above variables
export TCL_INCLUDE_DIR=$EBROOTTCL/include
export TCL_LIBRARY_DIR=$EBROOTTCL/lib

if true; then # disable/enable build plugins
  cd $BUILDDIR/vmd-$VMD_VERSION
   ./configure LINUXAMD64 NOSILENT ICC OPENGL OPENGLPBUFFER FLTK TK TCL PTHREADS NETCDF PYTHON NUMPY XINPUT XINERAMA LIBOSPRAY LIBOPTIX CUDA IMD LIBTACHYON
   # more:  COLVARS VRPN LIBSBALL ACTC FREEVR
  cd ./src
  make
  make install
fi
}}}