Version 1 (modified by 7 years ago) ( diff ) | ,
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!!! 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.
1. Build
- General build instructions can be found 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 # 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 # 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 false; then # disable/enable build plugins cd $BUILDDIR/plugins make clean make LINUXAMD64 TCLINC=$TCLINC TCLLIB=$TCLLIB NETCDFINC=$NETCDFINC NETCDFLIB=$NETCDFLIB EXPATINC=$EXPATINC EXPATLIB=$EXPATLIB make distrib fi ########## BUILD VMD export VMDINSTALLBINDIR=$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 false; 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 # more: COLVARS IMD VRPN LIBSBALL ACTC LIBTACHYON cd ./src make make install fi
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- vmd-1.9.3_configure.patch (7.1 KB ) - added by 7 years ago.
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