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

VMD - Visual Molecular Dynamics

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.

• ​VMD (Visual Molecular Dynamics)

Prebuild on JURECA

VMD is prebuild on JURECA.
Please use the graphical login to JURECA (more infos) to use VMD.

• You can find a VMD icon on the 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 HERE​.

• VMD was build on JURECA using EasyBuild similar to the following script:

  #!/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